Re: [Freesurfer] hippocampal subfields analysis took 10 min
Hi Jiook, That is a bit weird. What was the error that you got on the left hemisphere? In any case, 10 mins sounds about right. Does the output segmentation look ok? Cheers, Eugenio Juan Eugenio Iglesias Honorary Senior Research Associate Translational Imaging Group University College London and Postdoctoral researcher BCBL http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jiook Cha" <cha.ji...@gmail.com> To: "Eugenio Iglesias" <e.igles...@bcbl.eu>, "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Saturday, May 21, 2016 1:33:59 PM Subject: hippocampal subfields analysis took 10 min Dear Eugenio, I had to run the hippocampal subfield segmentation analysis in Freesurfer v6 manually by running segmentSF_T1.sh program. When I call it through recon-all, it only processed the left hemisphere but not the right. The issue is that running segmentSF only took 10 min per hemisphere. I didn't use multicores. Although the analysis resulted in all the files correctly, I am just concerned if running this manually completed the analysis prematurely. Sincerely, Jiook ᐧ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] segfault using brainstem module from dev version
It seems that mri_robust_register crashed. Martin, any ideas? The algorithm worked because the rough registration from the previous step was apparently enough to yield a decent segmentation. Maybe we should consider stopping the whole process if mri_robust_register dies... Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Vincent Beliveau" <vincent.beliv...@nru.dk> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, May 13, 2016 2:40:11 PM Subject: [Freesurfer] segfault using brainstem module from dev version Hi list (and Eugenio), I've ran the brainstem module from the dev version on some data processed with FS v5.3. The module created some great segmentations of brainstem but when taking a closer look at the log file, there is 2 seg faults which occur when calls to mri_robust_register are made, with the following output (full log attached, see line 319 and 371): /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register: line 3: 36835 Segmentation fault mri_robust_register.bin "$@" /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register --mov imageDump.mgz --dst /indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: Segmentation fault mv: cannot stat ?imageDump_coregistered.mgz?: No such file or directory I'm curious about how is this affecting the overall process, as otherwise everything appears to be working smoothly. Best, Vincent. -- Vincent Beliveau, MSc Neurobiology Research Unit Juliane Maries Vej 28, 3rd floor Rigshospitalet, building 6931 DK-2100 Copenhagen, Denmark phone: +45 3545 6718 e-mail: vincent.beliv...@nru.dk ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Manual correction for brainstem module
Yes! But take all the medulla volumes from the script. In other words: do not use the script to compute the medulla volumes of the cases you edited, and take the medulla volumes from the text file for all other cases. If you do that, you'd be introducing a fairly ugly bias in the study. Cheers, /E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee" <cyle...@gmail.com> To: "Eugenio Iglesias" <e.igles...@bcbl.eu> Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, May 12, 2016 4:11:20 PM Subject: Re: [Freesurfer] Manual correction for brainstem module Hi Eugenio, Thanks, the script worked. Actually I only edited the medulla segmentation in 3 out of the 49 subjects that I have. I suppose the original volumetric estimates for midbrain and pons are still valid and I can just calculate and compare the new medulla volumes for all subjects. Is that correct? Jacky 2016-05-12 12:05 GMT+02:00 Eugenio Iglesias < e.igles...@bcbl.eu > : My email client is replacing the combination colon + right parenthesis by a smiley! If the same thing happened to you, please replace the smiley by a colon and a right parenthesis... Next time I'll just attach the code. Sorry for the inconvenience Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Eugenio Iglesias" < e.igles...@bcbl.eu > To: "Jacky Lee" < cyle...@gmail.com > Cc: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, May 12, 2016 5:59:33 AM Subject: Re: [Freesurfer] Manual correction for brainstem module Of course! I haven't tested the code below, but I think it should work right away. Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if not, replace the location in the code below). Also, you'd need to replace the name of your subject directory. Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and saved as brainstemSsLabels.v10.edited.mgz (again, replace as needed). subjectdir='/mysubjectdir/'; editedFileName='brainstemSsLabels.v10.edited.mgz'; addpath /usr/local/freesurfer/matlab d=dir(subjectdir); for i=1:length(d) tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName]; if d(i).isdir && exist(tentativeSegFile,'file') A=MRIread(tentativeSegFile); MidbrainVol=8*sum(A.vol(:)==173); % the eight is because each voxel of the segmentation has a volume equal to 0.125 cubic mm PonsVol=8*sum(A.vol(:)==174); MedullaVol=8*sum(A.vol(:)==175); SCPvol=8*sum(A.vol(:)==178); disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ', pons = ' num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = ' num2str(SCPvol)]); end end One more thing: if you haven't edited anything around the SCP, I would use the original estimate for this structure. The reason is that, because the SCP is very thing, the voxel count is a much poorer approximation for the volume as computed by the code (i.e., using soft segmentations). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee" < cyle...@gmail.com > To: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > Cc: "Eugenio Iglesias" < e.igles...@bcbl.eu > Sent: Thursday, May 12, 2016 10:32:24 AM Subject: Re: [Freesurfer] Manual correction for brainstem module Hi Eugenio, Yes please give me some advice on the matlab commands for this since I am not very familiar with matlab... Cheers, Jacky Hi Jacky, this is a good question, and unfortunately there isn't a great answer to it. The volume is computed upong a probabilitic segmentation of the voxels that is not written to disk (this is very similar to what happens with aseg.mgz and aseg.stats). In order to properly update the volume estimates, you would have to know the probability that the inpainted voxels belong to the brainstem as estimated by the algorithm, which we don't currently write to disk. Another option would be to toss the volumes given by the algorithm, and compute new volumes for all cases and brainstem structures using the hard segmentations. You would simply have to count the number of voxels labeled as midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. with Matlab (let me know if you need help with this). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee"
Re: [Freesurfer] Manual correction for brainstem module
My email client is replacing the combination colon + right parenthesis by a smiley! If the same thing happened to you, please replace the smiley by a colon and a right parenthesis... Next time I'll just attach the code. Sorry for the inconvenience Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Eugenio Iglesias" <e.igles...@bcbl.eu> To: "Jacky Lee" <cyle...@gmail.com> Cc: "Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, May 12, 2016 5:59:33 AM Subject: Re: [Freesurfer] Manual correction for brainstem module Of course! I haven't tested the code below, but I think it should work right away. Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if not, replace the location in the code below). Also, you'd need to replace the name of your subject directory. Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and saved as brainstemSsLabels.v10.edited.mgz (again, replace as needed). subjectdir='/mysubjectdir/'; editedFileName='brainstemSsLabels.v10.edited.mgz'; addpath /usr/local/freesurfer/matlab d=dir(subjectdir); for i=1:length(d) tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName]; if d(i).isdir && exist(tentativeSegFile,'file') A=MRIread(tentativeSegFile); MidbrainVol=8*sum(A.vol(:)==173); % the eight is because each voxel of the segmentation has a volume equal to 0.125 cubic mm PonsVol=8*sum(A.vol(:)==174); MedullaVol=8*sum(A.vol(:)==175); SCPvol=8*sum(A.vol(:)==178); disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ', pons = ' num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = ' num2str(SCPvol)]); end end One more thing: if you haven't edited anything around the SCP, I would use the original estimate for this structure. The reason is that, because the SCP is very thing, the voxel count is a much poorer approximation for the volume as computed by the code (i.e., using soft segmentations). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee" <cyle...@gmail.com> To: "Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu> Cc: "Eugenio Iglesias" <e.igles...@bcbl.eu> Sent: Thursday, May 12, 2016 10:32:24 AM Subject: Re: [Freesurfer] Manual correction for brainstem module Hi Eugenio, Yes please give me some advice on the matlab commands for this since I am not very familiar with matlab... Cheers, Jacky Hi Jacky, this is a good question, and unfortunately there isn't a great answer to it. The volume is computed upong a probabilitic segmentation of the voxels that is not written to disk (this is very similar to what happens with aseg.mgz and aseg.stats). In order to properly update the volume estimates, you would have to know the probability that the inpainted voxels belong to the brainstem as estimated by the algorithm, which we don't currently write to disk. Another option would be to toss the volumes given by the algorithm, and compute new volumes for all cases and brainstem structures using the hard segmentations. You would simply have to count the number of voxels labeled as midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. with Matlab (let me know if you need help with this). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee" < cyle...@gmail.com > To: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > Sent: Monday, May 9, 2016 2:01:53 AM Subject: [Freesurfer] Manual correction for brainstem module Hi freesurfer experts, I have successfully run the brainstem module for some subjects. On visual checking, I can see there are voxels with T1 hypointense lesions mislabelled as non-brainstem tissue. I manually corrected them on the brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected volume of the brainstem substructures? Thanks. Regards, Jacky ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and proper
Re: [Freesurfer] Manual correction for brainstem module
Of course! I haven't tested the code below, but I think it should work right away. Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if not, replace the location in the code below). Also, you'd need to replace the name of your subject directory. Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and saved as brainstemSsLabels.v10.edited.mgz (again, replace as needed). subjectdir='/mysubjectdir/'; editedFileName='brainstemSsLabels.v10.edited.mgz'; addpath /usr/local/freesurfer/matlab d=dir(subjectdir); for i=1:length(d) tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName]; if d(i).isdir && exist(tentativeSegFile,'file') A=MRIread(tentativeSegFile); MidbrainVol=8*sum(A.vol(:)==173); % the eight is because each voxel of the segmentation has a volume equal to 0.125 cubic mm PonsVol=8*sum(A.vol(:)==174); MedullaVol=8*sum(A.vol(:)==175); SCPvol=8*sum(A.vol(:)==178); disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ', pons = ' num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = ' num2str(SCPvol)]); end end One more thing: if you haven't edited anything around the SCP, I would use the original estimate for this structure. The reason is that, because the SCP is very thing, the voxel count is a much poorer approximation for the volume as computed by the code (i.e., using soft segmentations). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee" <cyle...@gmail.com> To: "Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu> Cc: "Eugenio Iglesias" <e.igles...@bcbl.eu> Sent: Thursday, May 12, 2016 10:32:24 AM Subject: Re: [Freesurfer] Manual correction for brainstem module Hi Eugenio, Yes please give me some advice on the matlab commands for this since I am not very familiar with matlab... Cheers, Jacky Hi Jacky, this is a good question, and unfortunately there isn't a great answer to it. The volume is computed upong a probabilitic segmentation of the voxels that is not written to disk (this is very similar to what happens with aseg.mgz and aseg.stats). In order to properly update the volume estimates, you would have to know the probability that the inpainted voxels belong to the brainstem as estimated by the algorithm, which we don't currently write to disk. Another option would be to toss the volumes given by the algorithm, and compute new volumes for all cases and brainstem structures using the hard segmentations. You would simply have to count the number of voxels labeled as midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. with Matlab (let me know if you need help with this). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky Lee" < cyle...@gmail.com > To: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > Sent: Monday, May 9, 2016 2:01:53 AM Subject: [Freesurfer] Manual correction for brainstem module Hi freesurfer experts, I have successfully run the brainstem module for some subjects. On visual checking, I can see there are voxels with T1 hypointense lesions mislabelled as non-brainstem tissue. I manually corrected them on the brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected volume of the brainstem substructures? Thanks. Regards, Jacky ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Brainstem segmentation
Dear Haque, FreeSurfer 6 has not been released yet. But if you want to try the brainstem segmentation module, you can download the dev version; you will find it in there. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Haque, Muhammad E" <muhammad.e.ha...@uth.tmc.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, May 2, 2016 5:24:48 PM Subject: [Freesurfer] Brainstem segmentation Dear FreeSurfer Users, I would like to know if we can do brainstem segmentation as described in the recent publication http://www.sciencedirect.com/science/article/pii/S1053811915001895 Author as well as FreeSurfer website mention that this feature is only available in FreeSurfer 6.0 and later version https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Where I can download this FreeSurfer 6.0? Thanks. Haque ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippo subfield segmentation new beta version (version 6)
Hi Barbara, Sorry for the late response. - the type of sequence does not matter much as long as the contrast between gray and white matter is good. - the resolution is important, because you need to be able to see the internal thin layer of white matter in the hippocampus to be able to infer its internal structure; otherwise, the segmentation of the internal boundarie will indeed be dominated by the prior knowledge, rather than the intensities. - the algorithm operates at 0.33mm (isotropic) resolution; the segmentation is provided both at that resolution and at 1mm isotropic (FS space); please see the details in the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields If you send me the T2FLAIR and T2STIR images for a sample subject, I can take a look and give you more accurate answers ;-) Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Barbara Kreilkamp" <bakk@googlemail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, April 22, 2016 5:28:44 PM Subject: [Freesurfer] hippo subfield segmentation new beta version (version 6) Dear all, Would you please help me on this one? Thank you, best wishes, Barbara Forwarded Message Subject:hippo subfield segmentation new beta version (version 6) Date: Wed, 20 Apr 2016 11:45:02 +0100 From: Barbara Kreilkamp <bakk@gmail.com> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Dear all, I've been reading the manuscript on version 6 freesurfer hippocampal subfield segmentation "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: application to adaptive segmentation of in vivo MRI" Can you please tell me if the type of sequence (e.g. coronal T2FLAIR vs T2STIR) and voxel sizes of .4x.4x2mm^3 vs .4x.4x4mm^3 really make a difference for this multi-modal algorithm? I previously ran recon-all on 1mm isotropic T1-w scans all with similar contrast. It seems that the mesh fitting in version 6 is driven by the relation of the subfields to each other rather than by contrast or signal intensities; and also I notice the algorithm brings everything to isotropic space anyway. Is this correct? Do you see a major methodological issue when using T2FLAIR (.4x.4x4mm^3) and T2STIR (.4x.4x2mm^3) subfield volumes together? Thank you very much, Best wishes, Barbara P.s. as a side-note, I've not noticed any major differences in subfield segmentations visually, when comparing segmentations via these two different T2 scans. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal subfields, stuck?
Dear Maximilià, first of all, sorry for the late response. We assume throughout the code that mv a.ext b.ext will overwrite b.ext if it exists. If this is not the case in your system, maybe you could create an alias from 'mv' -> 'mv -f' before calling recon-all? Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "BAUTISTA-PERPINYA Maximilià" <maximila.bautista-perpi...@etu.unistra.fr> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, April 18, 2016 9:35:05 AM Subject: [Freesurfer] Hippocampal subfields, stuck? Dear all experts, I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1". Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter whether I say y or n; it seems it gets stuck and doesn't progress at all. There is no cpu usage. Any recommendations? I have attached the hippocampal subfields log. More info: - FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 - -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpi...@etu.unistra.fr maxbau...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CA2 hippocampal subfield in FS6.0
Yes! Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Patrick Sezen" <patrick.se...@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, April 18, 2016 7:20:46 PM Subject: [Freesurfer] CA2 hippocampal subfield in FS6.0 Dear FreeSurfers, I was running the FS 6.0 hippocampal subsegmentation and was wondering where the CA2 subfield disappeared to. Version 5.3 had a CA2-3 label, but in 6.0 I can only find CA3, is it implicated that CA2 is part of CA3 as well in 6.0? Sincerely, Patrick Sezen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer v6 beta
Hi again, in the paper, we used FreeSurfer 5.3 the process the data (recon-all), and then run the hippocampal module on top of that. So, with a bit of trouble, you can reproduce the results.. However, the 6.0 beta was taken down, so reproducing the results of the recon-all stream would be hard, and since such results affect the hippocampal module, reproducing the subfield segmentation would in turn also be hard. Does this make sense? Cheers, /E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Francis Tyson Thomas" <francisttho...@email.arizona.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, April 14, 2016 1:04:31 AM Subject: Re: [Freesurfer] Freesurfer v6 beta Hi Eugenio, I understood this part that you mentioned but I didn't understand how is is affected and what would be its consequences? Because I am referring to your preprint paper that makes use of v6, so will the results/validity of that paper also get affected by these differences. Because in my work the accuracy of the segmentation outputs are critical both for analysis and speeding it up. Thanks, Tyson On Wed, Apr 13, 2016 at 3:52 PM, Eugenio Iglesias < e.igles...@bcbl.eu > wrote: Hi Tyson, the hippocampal module shouldn't change between your beta and the FS6 release, but the main recon-all stream will. Since the latter is used to initialize the former, the results will be a bit different. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Francis Tyson Thomas" < francisttho...@email.arizona.edu > To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, April 13, 2016 8:19:18 PM Subject: [Freesurfer] Freesurfer v6 beta Hi, I was wondering when would the new Freesurfer v6 beta be available? Also I have been using the old beta for my hippocampal segmentation and I wanted to know if this new beta will affect the results of that? Thanks, Tyson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer v6 beta
Hi Tyson, the hippocampal module shouldn't change between your beta and the FS6 release, but the main recon-all stream will. Since the latter is used to initialize the former, the results will be a bit different. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Francis Tyson Thomas" <francisttho...@email.arizona.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, April 13, 2016 8:19:18 PM Subject: [Freesurfer] Freesurfer v6 beta Hi, I was wondering when would the new Freesurfer v6 beta be available? Also I have been using the old beta for my hippocampal segmentation and I wanted to know if this new beta will affect the results of that? Thanks, Tyson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Almost correct! recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp/I0001.dcm T2hipp Also, this is assuming that you have defined the environment variable SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd . Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Lara Foland-Ross" <lfol...@stanford.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, April 6, 2016 12:29:09 AM Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Hi Eugenio, Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely! Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags? For example, in my rawdata directory, I have two folders: subj1_T1 and subj1_hipp. I cd'd into the rawdata folder and ran the following with no success: recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp T2hipp Is this directory setup correct? And can you please point out the errors in the above recon-all command? Many thanks again for your help! Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.igles...@bcbl.eu> Sent: Tuesday, April 5, 2016 2:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Lara Foland-Ross" <lfol...@stanford.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Hello, I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain. My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned. I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands: mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV. Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss. Many thanks in advance, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this
Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Lara Foland-Ross" <lfol...@stanford.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Hello, I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain. My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned. I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands: mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV. Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss. Many thanks in advance, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] stacked iteration in brainstem segmentation
Hi again, Claudia. As a temporary workaround, you can use this flag in your recon-all command: -itkthreads 1 This will tell the code not to multithread, which will make it slower, but should help avoid the problems you have experienced. Please let us know how that goes! Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Claudia Testa" <claudia.te...@unibo.it> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, March 31, 2016 11:03:38 AM Subject: Re: [Freesurfer] stacked iteration in brainstem segmentation Hi Eugenio, we run the brainstem segmentation for 7 seven subjects and it succeded for 3 of them. Then we did not carry on with the others. The data are always 3D volumetric FSPGR acquired with the same sequence and scanner. Would you need any other info? Cheers, Claudia Da: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.igles...@bcbl.eu] Inviato: mercoledì 30 marzo 2016 18.56 A: Freesurfer support list Oggetto: Re: [Freesurfer] stacked iteration in brainstem segmentation Hi Claudia, Sorry for the late response. I am aware of this bug and I'm exploring possible solutions. How often does it happen in your data (i.e., how many subjects out of how many)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Claudia Testa" <claudia.te...@unibo.it> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, March 25, 2016 1:03:42 PM Subject: [Freesurfer] stacked iteration in brainstem segmentation Dear all, I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the -brainstem-structures option. The bug was solved downloading the new available version but I still have some problems. The recon-all -s subject -brainstem-structures stacks at a certain point (always the same one: "Iteration 2 of 7") for some subjects and for others it succeedes. In attach there is the log file for one successful segmentation (brainstem-structures_ok.log) and one for a failed segmentation (brainstem-structures.log). Can you help me? Thanks a lot Claudia 5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] stacked iteration in brainstem segmentation
In the hippocampal subfield segmentation, this happens once every 100-200 subjects. Three for seven is pretty bad. I'll take a look as soon as I can. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Claudia Testa" <claudia.te...@unibo.it> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, March 31, 2016 11:03:38 AM Subject: Re: [Freesurfer] stacked iteration in brainstem segmentation Hi Eugenio, we run the brainstem segmentation for 7 seven subjects and it succeded for 3 of them. Then we did not carry on with the others. The data are always 3D volumetric FSPGR acquired with the same sequence and scanner. Would you need any other info? Cheers, Claudia Da: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.igles...@bcbl.eu] Inviato: mercoledì 30 marzo 2016 18.56 A: Freesurfer support list Oggetto: Re: [Freesurfer] stacked iteration in brainstem segmentation Hi Claudia, Sorry for the late response. I am aware of this bug and I'm exploring possible solutions. How often does it happen in your data (i.e., how many subjects out of how many)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Claudia Testa" <claudia.te...@unibo.it> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, March 25, 2016 1:03:42 PM Subject: [Freesurfer] stacked iteration in brainstem segmentation Dear all, I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the -brainstem-structures option. The bug was solved downloading the new available version but I still have some problems. The recon-all -s subject -brainstem-structures stacks at a certain point (always the same one: "Iteration 2 of 7") for some subjects and for others it succeedes. In attach there is the log file for one successful segmentation (brainstem-structures_ok.log) and one for a failed segmentation (brainstem-structures.log). Can you help me? Thanks a lot Claudia 5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] stacked iteration in brainstem segmentation
Hi Claudia, Sorry for the late response. I am aware of this bug and I'm exploring possible solutions. How often does it happen in your data (i.e., how many subjects out of how many)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Claudia Testa" <claudia.te...@unibo.it> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, March 25, 2016 1:03:42 PM Subject: [Freesurfer] stacked iteration in brainstem segmentation Dear all, I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the -brainstem-structures option. The bug was solved downloading the new available version but I still have some problems. The recon-all -s subject -brainstem-structures stacks at a certain point (always the same one: "Iteration 2 of 7") for some subjects and for others it succeedes. In attach there is the log file for one successful segmentation (brainstem-structures_ok.log) and one for a failed segmentation (brainstem-structures.log). Can you help me? Thanks a lot Claudia 5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI BOLOGNA Codice Fiscale: 80007010376 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfield segmentation with T1
Hi Xiaowei, this was my mistake when I wrote the article in the wiki. The images do not need to be in the same orientation (I already changed this in the wiki). They need to be coarsely registered in physical coordinates (i.e., the need to look approximately registered when you open them in FreeView). If you manually rotate / translate the T2, make sure that you check the "do not resample" box when you save the rotated scan in order not to lose information. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> To: "Xiaowei Zhuang" <zhua...@ccf.org> Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, March 16, 2016 11:16:48 PM Subject: Re: [Freesurfer] Hippocampal subfield segmentation with T1 Hi Xiaowei you can try mri_robust_register --cost nmi or --cost mi, then give the resulting transform to mri_convert -at transform.lta -rl T2.mgz The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will have the same geometry. You can also try mri_coreg if you like instead of mri_robust_register if it doesn't work well cheers Bruce On Wed, 16 Mar 2016, Zhuang, Xiaowei wrote: > > Dear Freesurfer expert, > > > > I am using Freesurfer V6.0 beta version to run the hippocampal subfield > segmentation with 2 inputs, a standard T1 and a high resolution T2. > > > > Below are the details about the 2 images. > > > > T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8) > > T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5). > > > > The instruction says in order to use both of them for hippocampal > segmentation, T2 should be in the same orientation as T1. Therefore, the two > images cannot be used directly. > > > > Is it possible for me to do some reorient preprocess on the T2 image and > then run through the segmentation? > > > > Or is it possible to coregister the T1 into T2 space, making them both high > resolution and run through the segmentation? Will this affect the Freesurfer > pipeline and the final subfields output? > > > > Any suggestion will help. > > > > Sincerely thanks, > > Xiaowei. > > > > > > > > Cleveland Clinic logo > > > > Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain > Health > > Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV > 89106 | (702) 685-6051 > > > > > > === > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by > U.S.News & World Report (2015). Visit us online at > http://www.clevelandclinic.org for a complete listing of our services, staff > and locations. Confidentiality Note: This message is intended for use only > by the individual or entity to which it is addressed and may contain > information that is privileged, confidential, and exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient or the employee or agent responsible for delivering the message to > the intended recipient, you are hereby notified that any dissemination, > distribution or copying of this communication is strictly prohibited. If you > have received this communication in error, please contact the sender > immediately and destroy the material in its entirety, whether electronic or > hard copy. Thank you. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer 6.0
I only changed some details (e.g., temporary directories) that do not affect the output. Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, March 16, 2016 3:49:31 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 yes, although the hippocampal stuff hasn't changed I don't think (Eugenio: is that correct)? On Wed, 16 Mar 2016, Alan Francis wrote: > Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and > ran the HSF method successfully. Have they retracted that version? > > best, > > Alan > > On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > actually there is no beta yet, but hopefully within a week or so > On Wed, 16 Mar 2016, Alan Francis wrote: > > Hi Elizabeth: > > I ran the Hippocampal subfields on 6.0 beta. The > parcellation looks great. > Beta is available for download. Here is the URL: > > https://surfer.nmr.mgh.harvard.edu/fswiki/Download > > best, > > Alan > > On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul > <elisabeth.p...@student.uva.nl> wrote: > Dear ladies and gentlemen, > > for a research project I need to measure the volume > of the different > hippocampus subregions. I want to use FreeSurfer 6.0 > for that but I > can only find FreeSurfer 5.3 online. Is FreeSurfer > 6.0 not yet > released and if so, when will it be released? If it > is already > released, could you tell me where to find it? > > Thank you very much in advance. > > Kind regards, > > Elisabeth Paul > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for > the person to whom > it is > addressed. If you believe this e-mail was sent to > you in error and the > e-mail > contains patient information, please contact the > Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the > e-mail was sent to you > in error > but does not contain patient information, please > contact the sender > and properly > dispose of the e-mail. > > > > > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > Alan N. Francis PhD > NIDA T32 Fellow in Computational Neuroscience > Brain Imaging Center > McLean Hospital > Harvard Medical School > 115 Mill Street, Belmont, MA 02478 > al...@bwh.harvard.edu > afran...@mclean.harvard.edu > > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > Alan N. Francis PhD > NIDA T32 Fellow in Computational Neuroscience > Brain Imaging Center > McLean Hospital > Harvard Medical School > 115 Mill Street, Belmont, MA 02478 > al...@bwh.harvard.edu > afran...@mclean.harvard.edu > > &
Re: [Freesurfer] unknown option in new brainstem segmentation
Hi again, the brainstem module is at the end of the recon-all stream, and because recon-all stopped because of the error, the brainstem code never ran. Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Claudia Testa" <claudia.te...@unibo.it> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, March 10, 2016 1:02:26 PM Subject: Re: [Freesurfer] unknown option in new brainstem segmentation Hi Eugenio, yes the error seems in the option of mri_apar2aseg. I run as line in the shell: " mri_aparc2aseg --s 11960 --volmask -aseg aseg.presurf.hypos --annot aparc.DKTatlas40 " and it succeded. the recon-all -all command did not complete successfully, it stopped giving me the ERROR in the atlas option of mri_apar2aseg Claudia Da: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.igles...@bcbl.eu] Inviato: giovedì 10 marzo 2016 12.37 A: Freesurfer support list Oggetto: Re: [Freesurfer] unknown option in new brainstem segmentation Hi Claudia. Does the recon-all command complete successfully? The error seems to be in mri_aparc2aseg, right? Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Marmaduke" <marmaduke.wood...@univ-amu.fr> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, March 10, 2016 10:46:19 AM Subject: Re: [Freesurfer] unknown option in new brainstem segmentation On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa <claudia.te...@unibo.it> wrote: > >Dear Freesurfers, >I've installed Freesurfer 6.0 beta in a virtual machine, >and run the -brainstem-structures option to recon-all. > >The process stopped with an error: "ERROR: Option --DKTatlas40 >unknown" > >In the following, all the information: >_ >FREESURFER_HOME: /usr/local/freesurfer > >Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229 > >RedHat release: CentOS release 6.7 (Final) > >Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64 > >__ > >1) subject name is 11960 >2) the command line is: >recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz -s >11960 -brainstem-structures >3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos >--DKTatlas40 > >ERROR: Option --DKTatlas40 unknown >Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03 >UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > >recon-all -s 11960 exited with ERRORS at Wed Mar 9 23:53:10 CET 2016 > >4) in attach the recon-all.log file > > >Thank you for your help > >Claudia > > > > > >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom >it is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you >in error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. hi I had this as well, you have to rerun the last step manually with the correct atlas flag. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] unknown option in new brainstem segmentation
Hi Claudia. Does the recon-all command complete successfully? The error seems to be in mri_aparc2aseg, right? Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Marmaduke" <marmaduke.wood...@univ-amu.fr> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, March 10, 2016 10:46:19 AM Subject: Re: [Freesurfer] unknown option in new brainstem segmentation On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa <claudia.te...@unibo.it> wrote: > >Dear Freesurfers, >I've installed Freesurfer 6.0 beta in a virtual machine, >and run the -brainstem-structures option to recon-all. > >The process stopped with an error: "ERROR: Option --DKTatlas40 >unknown" > >In the following, all the information: >_ >FREESURFER_HOME: /usr/local/freesurfer > >Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229 > >RedHat release: CentOS release 6.7 (Final) > >Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64 > >__ > >1) subject name is 11960 >2) the command line is: >recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz -s >11960 -brainstem-structures >3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos >--DKTatlas40 > >ERROR: Option --DKTatlas40 unknown >Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03 >UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > >recon-all -s 11960 exited with ERRORS at Wed Mar 9 23:53:10 CET 2016 > >4) in attach the recon-all.log file > > >Thank you for your help > >Claudia > > > > > >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom >it is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you >in error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. hi I had this as well, you have to rerun the last step manually with the correct atlas flag. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] adc brainstem-subs
Dear Thomas, I am assuming that your ADC volume is defined in the voxel space of the other images in your subject directory (and that's why its dimensions are 256x256x256). In that case, you have two options: 1. Instead of using brainstemSsLabels.v10.mgz, you can use brainstemSsLabels.v10.1mm.mgz , which is defined in the same voxel space as the rest of your data. This is the easiest alternative. 2. If you want to work at higher resolution, you can also upsample your ADC data to the space of the brainstem segmentation. You can do this with: mri_convert [ADCvolume] [ADCvolumeResampled] -rl brainstemSsLabels.v10.mgz -odt float and then work with [ADCvolumeResampled] and brainstemSsLabels.v10.mgz Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Thomas Potrusil" <am-dam-...@gmx.at> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, March 10, 2016 9:17:19 AM Subject: [Freesurfer] adc brainstem-subs Dear FreeSurfers, I wan´t to extract adc values from newly segmented brainstem substructures by using mri_segstats --seg $brainstem_subs --ctab $FSCLUT --id 173 174 175 178 --seg-erode 1 --i $outdir_dtirecon/adc_anat.mgh --mul 1000 --sum $outdir_stat/adc_brainstem_subs.stats However, based on the fact that the seg volume is much smaller (173x221x140) than my input adc-file (256x256x256) I get an ERROR: dimension mismatch between input volume and seg !! Do you have any suggestions to overcome this problem? Thanks in advance, TomP ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippocampus subfields
OK now I get it ;-) You can simply do: mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl [lr]h.hippoSfLabels-T1-T2.v10.mgz The rl flag says: "reslice like the following volume" Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Prabesh Kanel" <pk...@my.fsu.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, March 2, 2016 8:31:17 PM Subject: Re: [Freesurfer] hippocampus subfields Hi Eugenio, Thank you, for your quick reply. It has happened to me in 4% of the cases, but my data sample is small like 100 data points. Addition to the second question: When I segment the hippocampus, I get the discrete segmentation volume at 0.333 mm resolution in the file [lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each voxel is labelled based on the subfield. I can use mri_extract_label or mri_binarize to extract individual subfield. But this segmentation will have voxels with the original label. If I load the file along with the T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the intensities at this place, I believe the intensity value is from T2.FSspace.mgz. Are those intensities values different from the original T2 images? If not, Is it possible to get those value at each voxel location? Best Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.igles...@bcbl.eu> Sent: Wednesday, March 2, 2016 12:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampus subfields Hi Prabesh, I think this is due to a bug that I found recently and which I'm trying to track down. Has it happened to you with many scans? The failure rate is less than 1% in my data. Regarding your second question: I'm sure it's not too trivial ;-) but I don't understand exactly what you mean. Do you want to deform the segmentations back to the original T2 space? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Prabesh Kanel" <pk...@my.fsu.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, March 2, 2016 6:07:13 PM Subject: [Freesurfer] hippocampus subfields Freesurfer List, I ran recon-all to segment hippocampus subfield using the development version of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and T2 images. But for some of the scans, the process stops at a point and doesn't seem to progress further. That happens in only a few cases and only when the data are run using the flag -hippocampal-subfields-T1T2. I have attached a log file of one of the case in this email. Another query that I have is to get T2 segmented subfields images (one with intensity values rather than labels). Is there an easier way to get T2 subfields segmented images using the segmentation volumes and T2.FSspace.mgz. Sorry, if this question seems too trivial. Regards, Prabesh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was se
Re: [Freesurfer] hippocampus subfields
Hi Prabesh, I think this is due to a bug that I found recently and which I'm trying to track down. Has it happened to you with many scans? The failure rate is less than 1% in my data. Regarding your second question: I'm sure it's not too trivial ;-) but I don't understand exactly what you mean. Do you want to deform the segmentations back to the original T2 space? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Prabesh Kanel" <pk...@my.fsu.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, March 2, 2016 6:07:13 PM Subject: [Freesurfer] hippocampus subfields Freesurfer List, I ran recon-all to segment hippocampus subfield using the development version of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and T2 images. But for some of the scans, the process stops at a point and doesn't seem to progress further. That happens in only a few cases and only when the data are run using the flag -hippocampal-subfields-T1T2. I have attached a log file of one of the case in this email. Another query that I have is to get T2 segmented subfields images (one with intensity values rather than labels). Is there an easier way to get T2 subfields segmented images using the segmentation volumes and T2.FSspace.mgz. Sorry, if this question seems too trivial. Regards, Prabesh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal subfield segmentation in FS 6.0
Hi Sarah, It's perfectly fine. Ideally, one would process everything with the same version so results are more easily reproducible but, since there's no FS 6.0 available yet, this is probably your best option for now, actually. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Sarah Lancaster" <sarah.lancas...@duke.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, February 17, 2016 3:39:16 PM Subject: [Freesurfer] Hippocampal subfield segmentation in FS 6.0 Hi all, We are running hippocampal subfield segmentations on about 300 subjects. We initially ran recon-all using FreeSurfer 5.3, but we used the new FreeSurfer 6.0 method for the hippocampal subfields. Will this cause problems in our analysis? Should we run them through recon-all again with 6.0? Thanks, Sarah Sarah Lancaster Research Assistant Duke-UNC Brain Imaging and Analysis Center Mental Illness Research, Education and Clinical Center Durham VA Medical Center sarah.lancas...@dm.duke.edu 919-286-0411 x7660 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Middle cerebellar peduncle segmentation
Dear Henri, As of today, there's no plan to add any new labels to the brainstem atlas. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Henri Pazro" <hpa...@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, February 10, 2016 6:27:47 PM Subject: [Freesurfer] Middle cerebellar peduncle segmentation Dear experts, I'm trying the brainstem segmentation from Juan Eugenio Iglesias and would like to know if the middle cerebellar peduncle will be added in a near future? Thanks! H. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Brain stem segmentation-- FS6
Hi Mohamad, you might have run out of memory. Could you please try allocating more RAM for the job? Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Mohamad J. Alshikho" <malshi...@mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, February 4, 2016 11:01:50 PM Subject: [Freesurfer] Brain stem segmentation-- FS6 Dear Freesurfer experts, I am working on brain stem segmentation analysis using the new module included in FS6. The analysis ran properly for 38/40 subjects. I have an issue with two subjects. I sent my jobs to the cluster as always using the following command line: pbsubmit -c " recon-all -subjid -brainstem-structures " -f & After a while I received an email that the job is done: PBS Job Id: 11020983.launchpad.nmr.mgh.harvard.edu Job Name: pbsjob_2045 Exec host: compute-0-111/3 Execution terminated Exit_status=0 resources_used.cput=00:42:33 resources_used.mem=3220236kb resources_used.vmem=7319444kb resources_used.walltime=00:44:45 I checked the subject's folder /mri/ looking for the files : "brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" but I was unable to find them. I checked the job history in the cluster and it returns as ( quotation -- the last lines): Resolution level 3 iteration 3 deformation iterations 19 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.0097272 voxels in 4.1676 seconds minLogLikelihoodTimesPrior = 1.0786e+07 Resolution level 3 iteration 3 deformation iterations 20 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.016365 voxels in 4.1717 seconds minLogLikelihoodTimesPrior = 1.0786e+07 Fitting mesh to image data mask took 2144.0218 seconds Error using kvlAtlas3D_Matlab std::bad_alloc Error in kvlRasterizeAtlasMesh (line 11) Error in segmentSubject (line 1078) Started at Thu Feb 4 15:57:18 EST 2016 Ended at Thu Feb 4 16:41:59 EST 2016 #@#%# recon-all-run-time-hours 0.745 recon-all -s CTRL039 finished without error at Thu Feb 4 16:42:00 EST 2016 It stated that the job was ended properly without errors but the previous lines ( before the final stamp) showed errors and the files "brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" are missing ... Kindly what I am doing wrong? Any suggestions are highly appreciated !! Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] HSF in 5.3
Got it! All you need to do is to replace Smoke_e024 by T1, which is the ID of the analysis: quantifyHippocampalSubfields.sh T1 Nicotine_HSF.txt Let me know if it doesn't work! Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Alan Francis" <alandarkene...@gmail.com> To: "Eugenio Iglesias" <e.igles...@bcbl.eu>, "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, January 29, 2016 4:17:06 PM Subject: Re: HSF in 5.3 Hi Eugenio: Here is the list of files in the 'mri' directory of a given subject: afrancis-mac:HSF afrancis$ cd Smoke_d004/ afrancis-mac:Smoke_d004 afrancis$ cd mri afrancis-mac:mri afrancis$ ls -la total 93464 drwxrwxr-x 47 afrancis staff 1598 Dec 23 01:05 . drwxr-xr-x 13 afrancis staff 442 Dec 22 13:14 .. -rw-r--r--@ 1 afrancis staff 6148 Dec 18 15:11 .DS_Store -rwxrw-rw- 1 afrancis staff 0 Dec 8 16:52 .xdebug_mris_calc -rw-rw-r-- 1 afrancis staff 5497095 Dec 22 13:25 T1.mgz -rw-rw-r-- 1 afrancis staff 387540 Dec 22 23:27 aparc+aseg.mgz -rw-rw-r-- 1 afrancis staff 418008 Dec 22 23:29 aparc.a2009s+aseg.mgz -rw-rw-r-- 1 afrancis staff 223392 Dec 22 17:35 aseg.auto.mgz -rw-rw-r-- 1 afrancis staff 1545 Dec 22 17:06 aseg.auto_noCCseg.label_intensities.txt -rw-rw-r-- 1 afrancis staff 222988 Dec 22 17:34 aseg.auto_noCCseg.mgz -rw-rw-r-- 1 afrancis staff 328176 Dec 22 23:29 aseg.mgz -rw-rw-r-- 1 afrancis staff 223419 Dec 22 23:25 aseg.presurf.hypos.mgz -rw-rw-r-- 1 afrancis staff 223392 Dec 22 17:35 aseg.presurf.mgz -rw-rw-r-- 1 afrancis staff 1245108 Dec 22 17:39 brain.finalsurfs.mgz -rw-rw-r-- 1 afrancis staff 1245108 Dec 22 17:39 brain.mgz -rw-rw-r-- 1 afrancis staff 1248043 Dec 22 13:43 brainmask.auto.mgz -rw-rw-r-- 1 afrancis staff 1248043 Dec 22 13:43 brainmask.mgz -rw-rw-r-- 1 afrancis staff 482728 Dec 22 14:08 ctrl_pts.mgz -rw-rw-r-- 1 afrancis staff 129128 Dec 22 17:43 filled.mgz -rw-rw-r-- 1 afrancis staff 69210 Dec 23 00:36 lh.hippoSfLabels-T1.v10.T1space.mgz -rw-rw-r-- 1 afrancis staff 66085 Dec 23 00:36 lh.hippoSfLabels-T1.v10.mgz -rw-rw-r-- 1 afrancis staff 286 Dec 23 00:36 lh.hippoSfVolumes-T1.v10.txt -rw-rw-r-- 1 afrancis staff 107428 Dec 22 23:13 lh.ribbon.mgz -rw-rw-r-- 1 afrancis staff 20564 Dec 22 13:51 mri_nu_correct.mni.log -rw-rw-r-- 1 afrancis staff 17647 Dec 22 13:22 mri_nu_correct.mni.log.bak -rw-rw-r-- 1 afrancis staff 1314015 Dec 22 14:08 norm.mgz -rw-rw-r-- 1 afrancis staff 3901730 Dec 22 13:51 nu.mgz -rw-rw-r-- 1 afrancis staff 2735369 Dec 22 16:29 nu_noneck.mgz drwxrwxr-x 3 afrancis staff 102 Dec 8 15:38 orig -rw-rw-r-- 1 afrancis staff 6690110 Dec 22 13:14 orig.mgz -rw-rw-r-- 1 afrancis staff 6922353 Dec 22 13:22 orig_nu.mgz -rwxrw-r-- 1 afrancis staff 10717567 Dec 22 13:14 rawavg.mgz -rw-rw-r-- 1 afrancis staff 69132 Dec 23 01:05 rh.hippoSfLabels-T1.v10.T1space.mgz -rw-rw-r-- 1 afrancis staff 62976 Dec 23 01:05 rh.hippoSfLabels-T1.v10.mgz -rw-rw-r-- 1 afrancis staff 286 Dec 23 01:05 rh.hippoSfVolumes-T1.v10.txt -rw-rw-r-- 1 afrancis staff 109623 Dec 22 23:13 rh.ribbon.mgz -rw-rw-r-- 1 afrancis staff 203963 Dec 22 23:13 ribbon.mgz -rw-rw-r-- 1 afrancis staff 119 Dec 22 17:40 segment.dat -rw-rw-r-- 1 afrancis staff 1545 Dec 22 15:02 talairach.label_intensities.txt -rw-rw-r-- 1 afrancis staff 214 Dec 22 14:05 talairach.log -rw-rw-r-- 1 afrancis staff 214 Dec 22 13:42 talairach_with_skull.log -rw-rw-r-- 1 afrancis staff 214 Dec 22 16:51 talairach_with_skull_2.log drwxrwxr-x 13 afrancis staff 442 Dec 22 17:35 transforms -rw-rw-r-- 1 afrancis staff 382039 Dec 22 17:42 wm.asegedit.mgz -rw-rw-r-- 1 afrancis staff 382750 Dec 22 17:42 wm.mgz -rw-rw-r-- 1 afrancis staff 415355 Dec 22 17:41 wm.seg.mgz -rw-rw-r-- 1 afrancis staff 435034 Dec 22 23:39 wmparc.mgz thank you, Alan On Thu, Jan 28, 2016 at 5:14 PM, Eugenio Iglesias < e.igles...@bcbl.eu > wrote: Hi Alan, can you please list the files in the mri directory of any of the subjects and send me the output? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Alan Francis" < alandarkene...@gmail.com > To: "Eugenio Iglesias" < e.igles...@bcbl.eu > Cc: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, January 28, 2016 9:18:46 PM Subject: Re: HSF in 5.3 Hi Eugenio: As you advised, I ran the following command: afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024 Nicotine_HSF.txt Gathering results from subjects in: /Users/afrancis/Desktop/Connectome/HSF/ Using the suffix name: Smoke_e024 And writing them to: Nicotine_HSF.txt However, when I opened the Nicotine_HSF.txt, there was nothing there. The
Re: [Freesurfer] HSF in 5.3
Hi Alan, can you please list the files in the mri directory of any of the subjects and send me the output? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Alan Francis" <alandarkene...@gmail.com> To: "Eugenio Iglesias" <e.igles...@bcbl.eu> Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, January 28, 2016 9:18:46 PM Subject: Re: HSF in 5.3 Hi Eugenio: As you advised, I ran the following command: afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024 Nicotine_HSF.txt Gathering results from subjects in: /Users/afrancis/Desktop/Connectome/HSF/ Using the suffix name: Smoke_e024 And writing them to: Nicotine_HSF.txt However, when I opened the Nicotine_HSF.txt, there was nothing there. The Subjects directory is the same folder. Please advice - thanks so much, Alan On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias < e.igles...@bcbl.eu > wrote: Hi Alan, the subfield module is not present in 5.3; you'll need to download the development version (or wait until 6.0 is released, which should be pretty soon=. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Alan Francis" < alandarkene...@gmail.com > To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu >, "eiglesias" < eigles...@bcbl.eu > Sent: Friday, December 11, 2015 6:36:42 PM Subject: HSF in 5.3 Hi Eugenio: I am trying to run the HSF method on 42 subjects. The FS version on our cluster is 5.3. However when I use the following command I get an error message. [alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields ERROR: Flag -hippocampal-subfields unrecognized. -s Smoke_d004 -hippocampal-subfields Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I tried adding the -hippocampal-subfields-T1 but that did not work too. thanks, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N . Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N . Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Dear Mohamad,
The brainstem module uses different anatomical definitions than aseg/wmparc,
and yes, the largest discrepancy is in the midbrain.
For the midbrain, I like the segmentation from the brainstem module better,
since it is based on manual annotations made by UCSF collaborators working
explicitly on the brainstem regions. But Bruce's opinion might be different?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Mohamad J. Alshikho" <malshi...@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, January 26, 2016 4:05:24 PM
Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Dear Freesurfers,
After segmenting the brain stem using FS6 tools. I used Free view to visualize
the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and
"brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by
flipping the images.
I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an
output of brain stem segmentation).
I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments.
Now After segmenting the brain stem. I see that the Ventral DC belongs to the
mid brain.
Is this natural?
Thanks in advance for any suggestion!
Mohamad
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Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Here it is (open access)
http://www.sciencedirect.com/science/article/pii/S1053811915001895
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Mohamad J. Alshikho" <malshi...@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, January 26, 2016 4:25:35 PM
Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Bruce and Juan,
Thanks a lot for your quick answer. I have one more question please:
What are the anatomical definitions that the brain stem module uses in order to
segment the brain stem. If you can point me to a reference that can help me to
understand this point this will be great!!
Thanks again
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]
Sent: Tuesday, January 26, 2016 10:16 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Dear Mohamad,
The brainstem module uses different anatomical definitions than aseg/wmparc,
and yes, the largest discrepancy is in the midbrain.
For the midbrain, I like the segmentation from the brainstem module better,
since it is based on manual annotations made by UCSF collaborators working
explicitly on the brainstem regions. But Bruce's opinion might be different?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Mohamad J. Alshikho" <malshi...@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, January 26, 2016 4:05:24 PM
Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Dear Freesurfers,
After segmenting the brain stem using FS6 tools. I used Free view to visualize
the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and
"brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by
flipping the images.
I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an
output of brain stem segmentation).
I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments.
Now After segmenting the brain stem. I see that the Ventral DC belongs to the
mid brain.
Is this natural?
Thanks in advance for any suggestion!
Mohamad
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine
at
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but does not contain patient information, please contact the sender and
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] hippocampal subfields - multispectral segmentation with FLAIR
Ciao Luigi, I haven't tried FLAIR for images the subfields, but if you sent me a high-res FLAIR acquisition of the hippocampus, I could take a look. If you are doing T2, you could implement the procotol used in ADNI: coronal slices with 0.4x0.4 in plane resolution, with 2mm slice separation (ideally, you would position the box in an slightly oblique positions such that the coronal slices cut the hippocampus perpendicularly to it major axis). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Luigi Antelmi" <luigi.ante...@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, January 25, 2016 9:43:29 AM Subject: [Freesurfer] hippocampal subfields - multispectral segmentation with FLAIR Dear members, in our center we are evaluating whether to introduce a T2 into a protocol that, among others, already includes a T1 and a FLAIR sequences. Our main concern is to to maximize the information-to-duration ratio of the entire protocol. In order to improve the subfields' segmentation we read that it is better to add a T2 or "other" sequences. Will the FLAIR alone (+T1) can work well as the T2? If instead the T2 is preferable, what is the coarsest-but-still-informative resolution you suggest? Thank you for sharing your experience! Have a nice day, Luigi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] HippocampalSubfields only generates lh
Hi Jiook, the log file says that the analysis of the left side did complete. Were the output files written? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jiook Cha" <cha.ji...@gmail.com> To: "iglesias" <igles...@nmr.mgh.harvard.edu> Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, January 20, 2016 2:16:36 AM Subject: HippocampalSubfields only generates lh Hi Iglesias, I recently tried HippocampalSubfields in freesurfer 6.0. It only completed hippocampal segmentation for the left hemisphere, but not the right. Under scripts folder, recon-all.error says: /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label CMD /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 /ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left So it seems as left hippocampus failed the pipeline didn’t try the right hippocampus. Attached is hippocampal-subfields-T1.log. Do you have any idea what’s happening here? Best, Jiook The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] HippocampalSubfields only generates lh
Sorry, it wasn't clear from the previous email whether the left hemi had completed or not. Can you please send me the recon-all log file? Cheers, /E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jiook Cha" <cha.ji...@gmail.com> To: "Eugenio Iglesias" <e.igles...@bcbl.eu> Cc: "iglesias" <igles...@nmr.mgh.harvard.edu>, "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, January 21, 2016 12:32:46 PM Subject: Re: HippocampalSubfields only generates lh Yes they were. On Jan 21, 2016, at 06:14, Eugenio Iglesias < e.igles...@bcbl.eu > wrote: Hi Jiook, the log file says that the analysis of the left side did complete. Were the output files written? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jiook Cha" < cha.ji...@gmail.com > To: "iglesias" < igles...@nmr.mgh.harvard.edu > Cc: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, January 20, 2016 2:16:36 AM Subject: HippocampalSubfields only generates lh Hi Iglesias, I recently tried HippocampalSubfields in freesurfer 6.0. It only completed hippocampal segmentation for the left hemisphere, but not the right. Under scripts folder, recon-all.error says: /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label CMD /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 /ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left So it seems as left hippocampus failed the pipeline didn’t try the right hippocampus. Attached is hippocampal-subfields-T1.log. Do you have any idea what’s happening here? Best, Jiook The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal subfields
Hi Alan, If you only want volumes, you can use quantifyHippocampalSubfields.sh. If you want to use the segmentations for something else (eg building ROIs for functional or diffusion), then you need to look into the mgz segmentation files. Cheers Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alan Francis <alandarkene...@gmail.com> To: Juan Eugenio Iglesias <eigles...@bcbl.eu>, Freesurfer <freesurfer@nmr.mgh.harvard.edu> Sent: Tue, 19 Jan 2016 20:26:13 +0100 (CET) Subject: Hippocampal subfields Hi Eugenio: Hope all is well. I have a question. I have run the HSF algorithm on 32 brains and they ran smoothly without problems. I used only T1 scans. I did not have T2s. Now to extract the data, do I need to run the following: *.FSspace.mgz*: the additional scan, rigidly registered to the T1 data. *[lr]h.hippoSfLabels--.v10.mgz*: they store the discrete segmentation volume at 0.333 mm resolution in the physical space of the FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> T1 data (and therefore of the aligned scan *.FSspace.mgz* as well). *[lr]h.hippoSfLabels--.v10.1mm.mgz*: they store the discrete segmentation volume in the 1 mm FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> voxel space. *[lr]h.hippoSfVolumes--.v10.txt*: these text files store the estimated volumes of the subfields and of the whole hippocampi. Or can I go directly to : quantifyHippocampalSubfields.sh - Thanks so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FW: FW: problem with hard coded directory (/scratch)
Hi Fengji, Sorry for the late reply; I was on vacation and totally missed your question. The hippocampal subfield module uses /scratch to create temporary files if available. If not, it creates a directory under the tmp directory inside the subject directory. It was coded this way because in our system, because of the way the cluster is setup, writing to /scratch is way more efficient. For now, the only thing you can do is to enable writing permissions on /scratch, or deleting /scratch. For the future: maybe we should remove the /scratch check and go to the subject's tmp directory directly (Zeke, Nick, what do you think?) Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Fengji Geng" <ge...@umd.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, January 14, 2016 7:46:44 PM Subject: [Freesurfer] FW: FW: problem with hard coded directory (/scratch) Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you! - Fengji From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! - Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you give us specific examples of problem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > /scratch)" have been changed to "if (-dw /scratch)". However, there > are still a lot of binaries in the bin directory that match the string > "scratch", which cause the same error that I encountered before. I am > wondering if it is possible for you to fix '/scratch' in the bin > directory. > > Thank you! - Fengji ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal Subfields (6.0) Error
Dear Andrew,
sorry for the late reply.
Aren't there any error outputs for the two cases?
If not, would you mind uploading the subjects so I can take a look?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Andrew Schoen" <schoen.andr...@gmail.com>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, December 23, 2015 4:05:00 PM
Subject: [Freesurfer] Hippocampal Subfields (6.0) Error
Hi all,
We are running some hippocampal subfield segmentations for two independent
studies. They have already been processed through the standard pipeline (5.3),
so I was just running the following command:
recon-all -s ${subjectid} -hippocampal-subfields-T1
For both test cases, the processing seems to have halted (no more updates to
the log file), but the command keeps running. For one study, it trailed off
here:
Resolution level 1 iteration 2 deformation iterations 13
Number of Meshes: 1
Using CG optimizer
Did one deformation step of max. 0.00037944 voxels in 14.6033 seconds
minLogLikelihoodTimesPrior =
2.3442e+06
Resolution level 1 iteration 2 deformation iterations 14
Number of Meshes: 1
Using CG optimizer
Did one deformation step of max. 1.3541e-06 voxels in 3.5131 seconds
minLogLikelihoodTimesPrior =
2.3442e+06
Resolution level 1 iteration 2 deformation iterations 15
Number of Meshes: 1
Using CG optimizer
Did one deformation step of max. 0 voxels in 30.0807 seconds
minLogLikelihoodTimesPrior =
2.3442e+06
maximalDeformation is too small; stopping
Iteration 3 of 7
(eof)
and the other here:
Making Left-Accumbens-area map to reduced label 13
--
Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians parameters
Estimating typical intensities of molecular layer and alveus
For ML in T1, we assume gray with high N
In T2, we actually assume the same hypermean
Smoothing mesh collection with kernel size 1.50 ...Smoothing class: 0
Smoothing class: 1
Smoothing class: 2
Smoothing class: 3
Smoothing class: 4
Smoothing class: 5
Smoothing class: 6
Smoothing class: 7
Smoothing class: 8
Smoothing class: 9
Smoothing class: 10
Smoothing class: 11
Smoothing class: 12
Smoothing class: 13
done
numberOfImages = 2
Image: 0
Image: 2
Iteration 1 of 7
(eof)
Interestingly, for one study, we have T2-weighted images, and when I ran with
that (same subject as second log, above), it ran to completion fine.
Any idea what might be happening? Let me know if any other info would be
useful!
Thanks!
Andrew Schoen
Center for Healthy Minds
Waisman Center
University of Wisconsin - Madison
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Re: [Freesurfer] HSF in 5.3
Hi Alan, the subfield module is not present in 5.3; you'll need to download the development version (or wait until 6.0 is released, which should be pretty soon=. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Alan Francis" <alandarkene...@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, "eiglesias" <eigles...@bcbl.eu> Sent: Friday, December 11, 2015 6:36:42 PM Subject: HSF in 5.3 Hi Eugenio: I am trying to run the HSF method on 42 subjects. The FS version on our cluster is 5.3. However when I use the following command I get an error message. [alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields ERROR: Flag -hippocampal-subfields unrecognized. -s Smoke_d004 -hippocampal-subfields Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I tried adding the -hippocampal-subfields-T1 but that did not work too. thanks, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N . Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Brainstem Substructures in Freesurfer 6.0 - how to calculate left/right volumes
Hi Chris, at this point, the software does not split the SCP into its left and right parts. But, you definitely gave me something to think about. When I have the time, I'll try to work on this and release a patch. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Chris Steward" <cstew...@unimelb.edu.au> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, December 10, 2015 1:53:58 AM Subject: [Freesurfer] Brainstem Substructures in Freesurfer 6.0 - how to calculate left/right volumes Hello, I've installed Freesurfer 6.0 beta, and run the -brainstem-structures option to recon-all. The results look ok, but I'd like the left/right volumes for the superior cerebellar peduncle (SCP), rather than the total volume. Is there any easy way to do this? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] -hippocampal-subfields-T1
Hi Daniele, do you think you could send us the subject? norm.mgz, wmparc.mgz and aseg.mgz should be enough. Also, have you experienced this problem with other subjects? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Daniele Orlandi" <daniele.orlandi@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, November 18, 2015 10:20:10 AM Subject: [Freesurfer] -hippocampal-subfields-T1 dear all, I'm running analysis with the new FS-v6.0 using the flag -hippocampal-subfields-T1 and I get the following error: none Matrix: -3.3 0 0 0 0 -3.3 0 3.3 0 Offset: [-34.0783, 128.423, -71.9905] Center: [0, 0, 0] Translation: [-34.0783, 128.423, -71.9905] Inverse: -0.3 0 0 0 0 0.3 0 -0.3 0 Singular: 0 I am WriteImage and I'm running! Wrote image to file asmr2.mgz This file does not contain MRI parameters Error using zeros NaN and Inf not allowed. Error in segmentSubjectT1_autoEstimateAlveusML (line 1396) MATLAB:nonaninf How I can solve it? Best, Daniele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons
Hi Andrew, it's perfectly possible. It would just make your results a bit harder to reproduce, but that's about it ;-) Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "O'Shea,Andrew" <aos...@ufl.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, November 18, 2015 3:07:04 PM Subject: [Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons Hello all, I was wondering if anyone with knowledge of the new hippocampal subfield segmentation that is going to be released with version 6.0 could answer a quick question. We have previously processed subjects in v5.3 and would like to use the new hippocampal seg algorithm. How “standalone” is the new process? Does the new process use any inputs from the recon-all stream which have changed in the upcoming version? Thanks! -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Advice for FreeSurfer developers
This is a good point. We should run the check right away. Right now, the subfield module runs at the end, which means that everything else has completed just fine, but we should definitely check at the very beginning and say: "either download the runtime or remove the subfield flag" Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Gronenschild Ed (NP)" <ed.gronensch...@maastrichtuniversity.nl> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, November 17, 2015 7:09:46 PM Subject: [Freesurfer] Advice for FreeSurfer developers Hi Doug, Yes, I know. It’s the hippocampal subfields segmentation that needs matlab runtime. Cheers, Ed On 17 Nov 2015, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 8 Date: Mon, 16 Nov 2015 12:52:20 -0500 From: Douglas N Greve < gr...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Advice for FreeSurfer developers To: freesurfer@nmr.mgh.harvard.edu Message-ID: < 564a17d4.6090...@nmr.mgh.harvard.edu > Content-Type: text/plain; charset=windows-1252; format=flowed Do you know what command was looking for matlab? On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote: BQ_BEGIN Hi Doug, I used mostly the default options, nothing special: recon-all -autorecon1 -clean-tal -expert my_options.txt -hires where the file my_options.txt contains some options for nu_correct. Then I entered recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires The error occurred with the last recon-all command. BTW, I really don't know if the -clean-tal option is needed with FS v6. Cheers Ed On 11 Nov 2015, at 18:00, < freesurfer-requ...@nmr.mgh.harvard.edu < mailto:freesurfer-requ...@nmr.mgh.harvard.edu >> wrote: BQ_BEGIN Message: 9 Date: Wed, 11 Nov 2015 11:08:46 -0500 From: Douglas Greve < gr...@nmr.mgh.harvard.edu < mailto:gr...@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To:freesurfer@ nmr.mgh.harvard.edu < mailto:freesurfer@nmr.mgh.harvard.edu > Message-ID: < 5643680e.1030...@nmr.mgh.harvard.edu < mailto:5643680e.1030...@nmr.mgh.harvard.edu >> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Ed, generally recon-all does not need matlab. Are you running the gyrification analysis? That should be the only thing that needs matlab. doug On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: BQ_BEGIN Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed ___ Freesurfer mailing list BQ_END BQ_END BQ_END ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] subfields segmentation FS v6.0
Ciao, Daniele, the alveus segmentation was very thin and unreliable, so we left it our of the results (even though it is still used in the model, and influences the fit of the atlas to the MRI scan). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Daniele Orlandi" <daniele.orlandi@gmail.com> To: "Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, November 3, 2015 12:36:30 PM Subject: [Freesurfer] subfields segmentation FS v6.0 Dear all I'm running the new pipleline for hippocampal subfields segmentation with FreeSurfer v6.0 on a T13D image. As results i can extract values for the Whole hippocampus and the following subfields: Hippocampal_tail, subiculum, CA1, hippocampal-fissure, presubiculum, parasubiculum, molecular_layer_HP, GC-ML-DG, CA3, CA4, fimbria, HATA but not for Alveus as reported in the paper of Iglesias, JE. et al. 2015. Was my computation wrong? Best, Daniele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippocampal subfield viewing
Hi Danielle, from the mri directory of a subject, run freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and be a bit patient; it takes a little while to combine all the posteriors into the segmentation. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Danielle Miller" <dmill...@bu.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, October 27, 2015 4:40:57 PM Subject: [Freesurfer] hippocampal subfield viewing Hello, I used recon-all -hippo subfields on an earlier version of free surfer (recon v 5.0, hippo v5.0 or 5.1). There is no documentation on your website on how to view the subfields in freeview with versions earlier than 5.2. I noticed when I load all the subfields into free view and use the color LUT file, the subfields have pixelated colors at each voxel. Is there a way to view earlier versions of this similar to what is presented on the website (i.e., where subfields are represented by solid colors)? I assume this may be an issue with intensity values in the image? Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] -hippocampal-subfields-T1T2
Hi Daniel, sorry for the late reply; I was on vacation. It seems that the T1-T2 registration failed. Can you please send me the .log files for the hippocampal subfields? They should be in the following directory: media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/scripts/ Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Daniele Orlandi" <daniele.orlandi@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, October 12, 2015 6:58:34 PM Subject: [Freesurfer] -hippocampal-subfields-T1T2 Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): > can't open file >No such file or directory >ERROR: Reading transform from file >/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta > Do you have any suggestion? thank you all for your collaboration Daniele ___ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel: +39 030/3501563 cell: +39 3495119685 email: dorla...@fatebenefratelli.it ; daniele.orlandi@gmail.com ( http://www.centroalzheimer.org/sito/chi_staff_e.php ) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampus visualisation
Hi Erik, one possible way of doing this: 1. For a single subfield: set the color map to Lookup Table. Tick "show as isosurface in 3d view". Tick "label volume". Then, set both values of the range to the numeric code of the subfield you want to display (e.g., for CA1, it would be 206). 2. For all subfields simultaneously: same as before, but setting the range to 200-226. This will color each subfield differently. 3. For showing the whole hippocampus in the same color: an easy, quick way is to switch the color map to grayscale, tick "show as isosurface in 3d view", untick "label volume", and set the lower and upper thresholds to 200 and 226, respectively. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Erik O'Hanlon" <erikohan...@rcsi.ie> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, October 2, 2015 10:31:17 AM Subject: [Freesurfer] Hippocampus visualisation Hi Freesurfer experts, I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all the subfields given in the table output? Sorry for the basic question, just trying to put together some images. Thanks in advance erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
This is really weird.
Can you please confirm that the file
/Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib
exists?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
Sent: Tuesday, September 29, 2015 11:39:00 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi Eugenio,
Thanks for the response. I just tried that and it still didn't work (same error
message).
Subject Stamp: freesurfer-Darwin-OSX-dev-20150826
Current Stamp: freesurfer-Darwin-OSX-dev-20150826
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r-- 1 lab wheel 638418 Sep 29 08:37
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log
Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
#
#@# Hippocampal Subfields processing (T1 only) left Tue Sep 29 08:39:10 PDT 2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left
\n
See log file:
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
40: 90075 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
#
#@# Hippocampal Subfields processing (T1 only) right Tue Sep 29 08:39:10 PDT
2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right
\n
See log file:
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
40: 90112 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
Thanks,
Aarthi
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias
<e.igles...@bcbl.eu>
Sent: Monday, September 21, 2015 1:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi Aarthi,
first of all, sorry for the late reply; you caught me on vacation.
Would you mind trying the following: please unset your DYLD_LIBRARY_PATH
environment variable, and the run the hippocampal subfield module. You can do
that as follows:
In bash:
unset DYLD_LIBRARY_PATH
In (t)csh:
unsetenv DYLD_LIBRARY_PATH
Let us know if this helps
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Aarthi Padmanabhan" <aar...@stanford.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Saturday, September 19, 2015 9:32:55 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi, I had posted this earlier and am still having issues.
Thank you,
I tried running the Hippocampal Segmentation using the Dev version, I get the
following error (running on a mac os x Yosemite):
I just downloaded the dev version a couple of days ago. Recon-all -all runs
fine, but it's unable to run the hippocampals segmentation component.
recon-all -s 15-03-07.1_3T2 -hippocampal-subfields-T1
Subject Stamp: freesurfer-Darwin-OSX-dev-20150826
Current Stamp: freesurfer-Darwin-OSX-dev-20150826
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-
Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi Aarthi,
first of all, sorry for the late reply; you caught me on vacation.
Would you mind trying the following: please unset your DYLD_LIBRARY_PATH
environment variable, and the run the hippocampal subfield module. You can do
that as follows:
In bash:
unset DYLD_LIBRARY_PATH
In (t)csh:
unsetenv DYLD_LIBRARY_PATH
Let us know if this helps
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Aarthi Padmanabhan" <aar...@stanford.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Saturday, September 19, 2015 9:32:55 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi, I had posted this earlier and am still having issues.
Thank you,
I tried running the Hippocampal Segmentation using the Dev version, I get the
following error (running on a mac os x Yosemite):
I just downloaded the dev version a couple of days ago. Recon-all -all runs
fine, but it's unable to run the hippocampals segmentation component.
recon-all -s 15-03-07.1_3T2 -hippocampal-subfields-T1
Subject Stamp: freesurfer-Darwin-OSX-dev-20150826
Current Stamp: freesurfer-Darwin-OSX-dev-20150826
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r-- 1 lab wheel 605436 Sep 11 11:56
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log
Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
#
#@# Hippocampal Subfields processing (T1 only) left Fri Sep 11 11:57:14 PDT
2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left
\n
See log file:
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
40: 6182 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
#
#@# Hippocampal Subfields processing (T1 only) right Fri Sep 11 11:57:15 PDT
2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right
\n
See log file:
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
40: 6219 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
#--
Started at Fri Sep 11 11:57:12 PDT 2015
Ended at Fri Sep 11 11:57:15 PDT 2015
#@#%# recon-all-run-time-hours 0.001
recon-all -s 15-03-07.1_3T2 finished without error at Fri Sep 11 11:57:15 PDT
2015
done
Thank you,
Aarthi
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Priyanka, in the mri directory of each subject, you will find a file named: [lr]h.hippoSfLabels--.v10.1mm.mgz which stores the discrete segmentation volume in the 1 mm FreeSurfer voxel space of that subject. Kind regards, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Priyanka Mehta" <priyankamehta0...@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Sunday, September 13, 2015 10:14:34 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi again I want to use my hippocampal segmentation for masking 2380 brain volumes. Is there a way to find out using Freesurfer if the hippocampal subfields and the 2380 volumes are in the same space? The mean of the 2380 volumes and the hippocampal subfields align correctly when I use Freesurfer's freeview to view them. But does that also mean they are in the same voxel space? And if they aren't in the same space, is there any way using Freesurfer that I can have the two in the same space? I really appreciate any suggestions! Thanks, Priyanka Mehta On Tue, Aug 25, 2015 at 4:50 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu > wrote: of course On Tue, 25 Aug 2015, Priyanka wrote: > Thanks Bruce. Just wanted to make sure I've got the correct output. > > Really appreciate the help. > > Thanks again, > Priyanka Mehta > >> On Aug 25, 2015, at 4:44 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu > >> wrote: >> >> Hi Priyanka >> >> that is what mri_extract_label is designed to do. This facilitates making >> density maps in a common space. If you want to get the original label # back >> you can use something like: >> >> mri_binarize --match 128 --binval or something like that >> >> cheers >> Bruce >> >> >>> On Tue, 25 Aug 2015, Priyanka Mehta wrote: >>> >>> Reposting my question: >>> This happens for all the segments that I've tried to extract using >>> mri_extract_label. They all show up as 128 nerve after mri_extract_label. >>> Is >>> this a bug in the dev version? >>> Any help is greatly appreciated! >>> On Thu, Aug 20, 2015 at 3:45 PM, Priyanka < priyankamehta0...@gmail.com > >>> wrote: >>> This happens for all the segments that I've tried to extract >>> using mri_extract_label. They all show up as 128 nerve after >>> mri_extract_label. Is this a bug in the dev version? >>> >>> > On Aug 20, 2015, at 3:20 PM, Lee Tirrell >>> < ltirr...@nmr.mgh.harvard.edu > wrote: >>> > >>> > It seems that the command: >>> > >>> > mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii >>> > >>> > put a value of 128 in lh.CA1.nii for the voxels labeled as 206 >>> in lh.hippoSfLabels-T1.v10.mgz. You can run: >>> > >>> > mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii >>> > >>> > and then the correct label names from the Lookup Table will >>> show up. >>> > >>> > Best, >>> > Lee >>> > >>> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote: >>> >> >>> >> Hi Eugenio >>> >> Thank you for the explanation, it makes sense to me now. >>> >> When I use Freeview to overlay my lh.CA1.nii on T1.nii, it >>> aligns correctly. However, when I view the segmentation >>> >> with color map set to Lookup Table and 'show existing labels >>> only' checked, the lh.CA1.nii segment shows as 128 Nerve >>> >> label. Shouldn't it still be showing up as 206 CA1 label? I >>> am confused. >>> >> >>> >> On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias >>> < e.igles...@bcbl.eu > wrote: >>> >> Hi Prya, >>> >> that is because MriCron is not that great at overlaying >>> images that are in the same physical space but not >>> >> in the same voxel space. You have two options here: >>> >> 1. Use FreeSurfer's Freeview rather than MriCron to >>> visualize the output. FreeView will correctly overlay >>> >> the segmentation. >>> >> 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than >>> lh.hippoSfLabels-T1.v10.mgz) when you call >>> >> mri_extract_label. That volume lives in the same voxel >>> space as T1.nii, and should be prope
Re: [Freesurfer] Scanner parameters for hippocampal subfield segmentation in Freesurfer 6.0
Hi Carl, this is hard to say in advance. Do you see the internal band (the "swiss roll" or "dark band") of the hippocampus in your scans? If so, then I would go for it. If not, I would trade a bit of slice separation for in-plane resolution. If you want, feel free to send me a capture of a representative coronal slice in the hippocampal body. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Carl Pintzka" <carl.pint...@ntnu.no> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, September 17, 2015 2:50:23 PM Subject: [Freesurfer] Scanner parameters for hippocampal subfield segmentation in Freesurfer 6.0 Hi, We are currently planning a population based MRI study and are interested in including a T2w scan that allows us to perform the new automatic hippocampal subfield segmentation included in Freesurfer 6.0. The current scanner settings (which has been used in a previous study) are as follows: 3T Siemens Skyra T2w turbo spin echo TR: 67 60, TE: 84 In plane resolution: 0.57x0.57mm Slice thickness: 1mm, no gap NAX: 3 In the Iglesias 2015 paper, 0.4x0.4 in plane resolution with 2mm slice thickness is used. Is this preferable since we intend on using the subfield segmentation on our dataset, or is it ok with 0.57x0.57 in plane resolution and thinner slices? We are not planning on performing manual segmentation on the dataset and thus want the settings to be optimal for the Freesurfer segmentation. What about number of averages? Best regards, Carl Pintzka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Alexandra, Thanks for your email. We have identified the problem an it will be fixed for the next build of our development version. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: Z K zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Cc: e iglesias e.igles...@bcbl.eu Sent: Thursday, August 20, 2015 2:29:16 PM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files? Hi Zeke and Eugenio, Thanks for your quick answers. I removed the maverick distribution and installed the lion one pointed by Zeke. Running the segmentation, I get the same message as before: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Here is were the symbolic link is pointing: segmentSubjectT1_autoEstimateAlveusML - ../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a It is pointing to a directory which is outside of freesurfer's. -Alexandra On 8/20/15 9:38 AM, Z K wrote: Hi Alexandra, The mavericks build that you downloaded was an experimental build that hasnt been updated for awhile. Please remove that version and download and install the lion version instead. That version is more up-to-date. Sorry for the confusion. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/20/2015 04:42 AM, Eugenio Iglesias wrote: Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeview
Page up / page down should work Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:16:13 PM Subject: [Freesurfer] Freeview Hi Freesurfers, I can’t change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the Up/ Down keys Thanks Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeview
Weird! The up and down arrows should move the current slice up and down, whereas page up/down should change the slice... You can also click on the other views to change the current slice. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:23:28 PM Subject: Re: [Freesurfer] Freeview Page up / down is moving the current slice up and down but it not flipping between the slices ?! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, August 19, 2015 12:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview Page up / page down should work Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:16:13 PM Subject: [Freesurfer] Freeview Hi Freesurfers, I can’t change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the Up/ Down keys Thanks Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Prya,
that is because MriCron is not that great at overlaying images that are in the
same physical space but not in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
FreeView will correctly overlay the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call mri_extract_label. That volume lives
in the same voxel space as T1.nii, and should be properly overlayed by MriCron.
However, the resolution of the segmentation will be 1 mm, rather than the 0.333
mm that you'd get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted the left CA1 using mri_extract_label
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the alignment is
not correct (see attached picture).
I wonder what is causing this issue? Since the CA1 was extracted from the same
T1 image, they should technically be in the same space and therefore should
align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta priyankamehta0...@gmail.com
wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
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contains patient information
Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
Hi Prabesh (et al), I installed Ubuntu 15.04 at home and unsetting JAVA_TOOL_OPTIONS solved the problem (in the end it worked for you, too, right?). Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 14, 2015 9:05:38 AM Subject: Re: [Freesurfer] segmentationfault while running -hippocampal-subfields-T1 flag Hi Eugenio, Thank you for your help. I saw your first email and tried running with JAVA_TOOL_OPTIONS and it worked. It is still running without segmentation fault. After I finish that one I will run with unset JAVA_TOOL_OPTIONS. I will let you know the result of second run. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.igles...@bcbl.eu Sent: Friday, August 14, 2015 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Sorry, I actually meant: unset JAVA_TOOL_OPTIONS Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Eugenio Iglesias e.igles...@bcbl.eu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 14, 2015 11:51:54 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi again, Prabesh would you mind trying this? It was a suggestions from a Mathworks representative. Please edit $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh and right under the line that says export XAPPLRESDIR;, please insert this line of code: JAVA_TOOL_OPTIONS If it doesn't work, I'll install Ubuntu 15 on my laptop this weekiend and do some more research Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 10, 2015 9:01:26 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi Eugenio, I have about 128 GB of RAM memory in both machine. I got segmentation fault error in the new machine and not in the older one. I ran the test data (bert) and I get segmentation fault error. I think the only difference between the two machine is Ubuntu version. The new machine uses Ubuntu 15.04 while the older one uses 14.04. Both the machine has the same hardware configuration. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.igles...@bcbl.eu Sent: Sunday, August 9, 2015 6:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail
Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
Hi again, Prabesh would you mind trying this? It was a suggestions from a Mathworks representative. Please edit $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh and right under the line that says export XAPPLRESDIR;, please insert this line of code: JAVA_TOOL_OPTIONS If it doesn't work, I'll install Ubuntu 15 on my laptop this weekiend and do some more research Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 10, 2015 9:01:26 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi Eugenio, I have about 128 GB of RAM memory in both machine. I got segmentation fault error in the new machine and not in the older one. I ran the test data (bert) and I get segmentation fault error. I think the only difference between the two machine is Ubuntu version. The new machine uses Ubuntu 15.04 while the older one uses 14.04. Both the machine has the same hardware configuration. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.igles...@bcbl.eu Sent: Sunday, August 9, 2015 6:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
Sorry, I actually meant: unset JAVA_TOOL_OPTIONS Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Eugenio Iglesias e.igles...@bcbl.eu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 14, 2015 11:51:54 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi again, Prabesh would you mind trying this? It was a suggestions from a Mathworks representative. Please edit $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh and right under the line that says export XAPPLRESDIR;, please insert this line of code: JAVA_TOOL_OPTIONS If it doesn't work, I'll install Ubuntu 15 on my laptop this weekiend and do some more research Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 10, 2015 9:01:26 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi Eugenio, I have about 128 GB of RAM memory in both machine. I got segmentation fault error in the new machine and not in the older one. I ran the test data (bert) and I get segmentation fault error. I think the only difference between the two machine is Ubuntu version. The new machine uses Ubuntu 15.04 while the older one uses 14.04. Both the machine has the same hardware configuration. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.igles...@bcbl.eu Sent: Sunday, August 9, 2015 6:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Regarding: Brainstem volumetric result
Hi Sampada, the two measurements are obtained through different methods. The aseg estimate is generally smaller because it doesn't include the whole midbrain, whereas the brainstem module does. Which one is more accurate depends on your anatomical definition of brainstem. Compared with the ASEG, the brainstem module has the advantage that it provides the parcellation into pons, medulla, midbrain and SCP. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Dr Sampada Sinha drsampadasi...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 12, 2015 3:52:36 PM Subject: [Freesurfer] Regarding: Brainstem volumetric result Dear freesurfer experts, I successfully managed to install and run the freesurfer dev version6 for brainstem segmentation analysis. But, looking at the result of brainstem volume in brainstemSsVolumes.v10.txt, the whole brainstem volume is 14439.355323 and the brainstem volume by recon-all out asegfile is 13217.8 in the same participant. Will you please let me know why this disparity is there? And which one is more accurate? We plan to use the medullary volume for our study (here the medullary volume of the participant is 3184.900208 ) Thanks and regards, Sampada -- Sampada Sinha AIIMS, New Delhi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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at
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properly
dispose of the e-mail.
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___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Re: [Freesurfer] mac installation problems
Hi Alison, what are your new errors (the ones you get almost immediately)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alison Austermuehle (NIH/NINDS) [F] alison.austermueh...@nih.gov To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 20, 2015 6:02:38 PM Subject: [Freesurfer] mac installation problems Hi, I am a new user of freesurfer. I have been running freesurfer on a Linux machine to look at hippocampal subfield volumes, but am now trying to switch over to a mac. I have installed the program, and it is located within /Applications/freesurfer. Ran the freesurfer source and export. When I tried to test the bert recon, I get this message: ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert When I do what the wiki suggests for admin issues ( sudo chmod -R a+w $FREESURFER_HOME/subjects/bert) , and try recon-all again, it quits with errors almost immediately. Note: I have full admin privileges on this computer. My goal is to take a folder with a long list of .dcm files and run a recon-all on it, which is currently on my desktop. Where does this folder need to be? Where is my subject directory? If someone with patience and generosity in their heart could help me out, using idiot-proof language, I would really appreciate it. Thanks, Alison Austermuehle NIH/NINDS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Regarding: Brainstem substructures
Hi Sampada, FS 6.0 is not out yet, but you can download the latest dev version from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ Using this version, you can run the brainstem module on subjects that have already been processed with 5.3. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Dr Sampada Sinha drsampadasi...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Saturday, July 11, 2015 6:37:12 PM Subject: Re: [Freesurfer] Regarding: Brainstem substructures Thanks so much Bruce for your reply. when I open the link for brain stem structures ( https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures ), it says This functionality is present in FreeSurfer 6.0 and later . And, when I go to the freesurfer download page, the only latest version of freesurfer (last updated by Zeke on 2015-06-02) I see is stable v5.3.0. If the version 6.0 is out, will you please send me the link so that I can download it? Thanks and regards, Sampada On Sat, Jul 11, 2015 at 7:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sampada the brainstem stuff was developed after 5.3 so it is likely not in the version you have. Eugenio or Zeke can point you in the right direction. cheers Bruce On Sat, 11 Jul 2015, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to do the brainstem volumetric analysis especially of the medullary region. My recon-all command ran successfully and now when I am trying to run the command ' recon-all -s IMRAN -brainstem-structures' ( https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures ) but, I get the following error: ERROR: Flag -brainstem-structures unrecognized. -s IMRAN -brainstem-structures Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Will you please let me know where I am going wrong? I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 version for my analysis. Thanks for your time! Kind regards, Sampada ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Angela, Of course it is! I'd be thrilled to see what you get out of your analyses; please keep me posted. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 13, 2015 11:21:30 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi Eugenio, I have a question about hippocampal segmentation. Do you think it is possible to use this segmentation to obtain specific seeds for a functional connectivity study? thank you Angela Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own
Re: [Freesurfer] Help with V6
Thanks Noah. It doea say on the website that you need the 2012b runtime, but its definitely buried among too much other, less critical stuff Cheers E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Sat, 04 Jul 2015 13:57:53 +0200 (CEST) Subject: Re: [Freesurfer] Help with V6 Hey Eugenio, I was able to resolve it with the help of another expert. One of the problems definitely was that 2014b doesn’t run on the hippocampal-subfields module. Maybe try adding that as a note to the website as numerous people have access to the 2014b version and 2015a was just released. Thanks again for all the help. Cheers, Noah On Jul 3, 2015, at 5:12 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote: Hi Noah, this error is pretty weird. Can you please send us the exact command you executed? Regarding the runtime: your 2014b runtime won't work. You need to follow the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 3, 2015 4:20:02 AM Subject: [Freesurfer] Help with V6 Hi, I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and source just as described for previous versions. Also, I have Matlab 2014b downloaded on the computer (obviously comes with runtime) but am unsure if the runtime folder needs to be placed in the FS folder or is fine where it is. Any FS experts help with these two problems and concerns? Much appreciated if you do. Cheers, Noah Markowitz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help with V6
Hi Noah, this error is pretty weird. Can you please send us the exact command you executed? Regarding the runtime: your 2014b runtime won't work. You need to follow the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 3, 2015 4:20:02 AM Subject: [Freesurfer] Help with V6 Hi, I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and source just as described for previous versions. Also, I have Matlab 2014b downloaded on the computer (obviously comes with runtime) but am unsure if the runtime folder needs to be placed in the FS folder or is fine where it is. Any FS experts help with these two problems and concerns? Much appreciated if you do. Cheers, Noah Markowitz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. run_segmentSubjectT1_autoEstimateAlveusML.sh Description: application/shellscript run_segmentSubjectT1T2_autoEstimateAlveusML.sh Description: application/shellscript run_segmentSubjectT2_autoEstimateAlveusML.sh Description: application/shellscript ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz
Hi Carl, the use of quantifyHippocampalSubfields.sh is: quantifyHippocampalSubfields.sh suffix outputFile [subjectsDirectory] Simply run quantifyHippocampalSubfields.sh T1 test_no-T1.txt or quantifyHippocampalSubfields.sh T1 test_no-T1.txt /Applications/freesurfer/subjects/RBrain and everything should work Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Carl Anderson remfr...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 10, 2015 6:54:55 PM Subject: [Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz Hi All, I have been using the quantifyHippocampalSubfields.sh from build 20150507 with no problems. However when I try to run the script in the new build (20150610) it fails if I run with the T1 flag or without. here is the result with T1: vermisii:RBrain carlanderson$ Gathering results from subjects in: test_T1.txt Using the suffix name: T1 And writing them to: subfieldAnalysis_T1_v1.0 /Applications/freesurfer/bin/quantifyHippocampalSubfields.sh: line 8: cd: test_T1.txt: No such file or directory failed to do cd test_T1.txt vermisii:RBrain carlanderson$ if I omit the T1 flag: vermisii:RBrain carlanderson$ quantifyHippocampalSubfields.sh subfieldAnalysis_T1_v1.0 test_no-T1.txt Gathering results from subjects in: /Applications/freesurfer/subjects/RBrain Using the suffix name: subfieldAnalysis_T1_v1.0 And writing them to: test_no-T1.txt vermisii:RBrain carlanderson$ Hope this helps, Carl -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com ; carl_ander...@hms.harvard.edu •~~•~~•~~•~~•~~•~~•~~• ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampal subfields
Hi Erik,
30 mins for a subject sounds correct. If the text files with the volumes are
there, and the segmentations look plausible, then everything should be fine.
One more thing: it the outputs are in specific directories, please note that we
changed the naming convention and structure of the output last week - sorry
about that! We believe that the changes made the module easier to use. Please
see the updated instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, May 27, 2015 10:17:51 AM
Subject: Re: [Freesurfer] hippocampal subfields
Hi Eugenio,
I managed to get the subfield code process to run, my cluster wasn't using all
the allotted RAM for the job, thank you for all the input. Can I ask how long
it typically takes as it appears to have completed in about 30mins and gave me
the left and right dirs with the volume txts etc. Just wanted to be sure before
I kick it off on the complete data set.
Thanks again for all the help.
Cheers
Ertik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]
Sent: 26 May 2015 11:25
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi again,
The software requires approximately 10GB of RAM
Cheers
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 26 May 2015 12:16:00 +0200 (CEST)
Subject: Re: [Freesurfer] hippocampal subfields
html
head
style!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left:
#80 2px solid; } --/style
/head
body
font size=2span style=font-size:10pt;
div class=PlainTextHi Eugenio,br
br
I#39;m trying to run in on a cluster and I think I have eight cores assigned
with 2GB per core. I#39;m not sure if the process is parallelised though so it
could be the case that I have the job running on one of the possible core and
only using 2GB of RAM. I can
ask the cluster support team to check but is it possible to run the job across
the 8 cores and thus grab the 16GB of RAM or will the code only use the
onenbsp; core and I will have to get the RAM assigned to it to be
increased.br
br
Any guidance much appreciated and maybe if you could outline a typical system
requirement/setup to run a job. I have 200 subjects so your advice would
super.br
br
Thanks againbr
br
Cheersbr
br
Erikbr
br
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]br
Sent: 26 May 2015 10:33br
To: Freesurfer support listbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
Hi Erik,br
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?br
Cheers,br
/Eugeniobr
br
Juan Eugenio Iglesiasbr
Postdoctoral researcher BCBLbr
a href= http://www.jeiglesias.com
target=_blankwww.jeiglesias.com/abr
a href= http://www.bcbl.eu target=_blankwww.bcbl.eu/abr
br
Legal disclaimer/Aviso legal/Lege-oharra: a href=
http://www.bcbl.eu/legal-disclaimer target=_blank
www.bcbl.eu/legal-disclaimer/abr
br
br
- Original Message -br
From: quot;Erik O#39;Hanlonquot; lt;erikohan...@rcsi.iegt;br
To: quot;Freesurfer support listquot;
lt;freesurfer@nmr.mgh.harvard.edugt;br
Sent: Monday, May 25, 2015 6:53:54 PMbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
br
br
Hi FS Experts,br
br
I#39;m trying the v6 hippocampal subfield code on a subject processed with
5.3.0 and I encountered the following error in the log filebr
br
Making Unknown map to reduced label 13br
Computing hyperparameters for estimation of Gaussian parametersbr
Estimating typical intensities of alveusbr
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 43: 2675 Killed
quot;${exe_dir}quot;/segmentSubjectT1_autoEstimateAlveusML $argsbr
~br
br
It appears that the process finished prematurely and didn#39;t write out
anything in the mri/ dir.br
br
Any pointers how to resolve ? Any help greatly appreciatedbr
Re: [Freesurfer] hippocampal subfields
Hi again,
The software requires approximately 10GB of RAM
Cheers
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 26 May 2015 12:16:00 +0200 (CEST)
Subject: Re: [Freesurfer] hippocampal subfields
html
head
style!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left:
#80 2px solid; } --/style
/head
body
font size=2span style=font-size:10pt;
div class=PlainTextHi Eugenio,br
br
I#39;m trying to run in on a cluster and I think I have eight cores assigned
with 2GB per core. I#39;m not sure if the process is parallelised though so it
could be the case that I have the job running on one of the possible core and
only using 2GB of RAM. I can
ask the cluster support team to check but is it possible to run the job across
the 8 cores and thus grab the 16GB of RAM or will the code only use the
onenbsp; core and I will have to get the RAM assigned to it to be
increased.br
br
Any guidance much appreciated and maybe if you could outline a typical system
requirement/setup to run a job. I have 200 subjects so your advice would
super.br
br
Thanks againbr
br
Cheersbr
br
Erikbr
br
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]br
Sent: 26 May 2015 10:33br
To: Freesurfer support listbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
Hi Erik,br
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?br
Cheers,br
/Eugeniobr
br
Juan Eugenio Iglesiasbr
Postdoctoral researcher BCBLbr
a href=http://www.jeiglesias.com; target=_blankwww.jeiglesias.com/abr
a href=http://www.bcbl.eu; target=_blankwww.bcbl.eu/abr
br
Legal disclaimer/Aviso legal/Lege-oharra: a
href=http://www.bcbl.eu/legal-disclaimer; target=_blank
www.bcbl.eu/legal-disclaimer/abr
br
br
- Original Message -br
From: quot;Erik O#39;Hanlonquot; lt;erikohan...@rcsi.iegt;br
To: quot;Freesurfer support listquot;
lt;freesurfer@nmr.mgh.harvard.edugt;br
Sent: Monday, May 25, 2015 6:53:54 PMbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
br
br
Hi FS Experts,br
br
I#39;m trying the v6 hippocampal subfield code on a subject processed with
5.3.0 and I encountered the following error in the log filebr
br
Making Unknown map to reduced label 13br
Computing hyperparameters for estimation of Gaussian parametersbr
Estimating typical intensities of alveusbr
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 43: 2675 Killed
quot;${exe_dir}quot;/segmentSubjectT1_autoEstimateAlveusML $argsbr
~br
br
It appears that the process finished prematurely and didn#39;t write out
anything in the mri/ dir.br
br
Any pointers how to resolve ? Any help greatly appreciatedbr
br
Cheersbr
br
Erikbr
br
Erik O#39;Hanlonbr
Postdoctoral researcherbr
br
br
br
br
RCSI Psychiatrybr
Royal College of Surgeons in Irelandbr
Beaumont Road, Beaumont, D9, Irelandbr
T: 8093740br
E: erikohan...@rcsi.ie W: a href=http://www.rcsi.ie;
target=_blankwww.rcsi.ie/abr
br
RCSI DEVELOPING HEALTHCARE LEADERSbr
WHO MAKE A DIFFERENCE WORLDWIDEbr
br
From: Erik O#39;Hanlonbr
Sent: 08 May 2015 19:10br
To: Freesurfer support listbr
Subject: RE: [Freesurfer] hippocampal subfieldsbr
br
That is super Nick,br
br
I#39;ll download it next week and try it out. Will I need to just run the
subfield part based on the 5.3.0 analysis I have or do it from scratch with the
beta v6?br
br
Thanks again for all the helpbr
br
Erikbr
br
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH
[ni...@nmr.mgh.harvard.edu]br
Sent: 08 May 2015 19:05br
To: Freesurfer support listbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
Erik,br
br
If you wanted to test a #39;beta#39; of v6, which has the new hippocampalbr
stream, then our current internal #39;dev#39; build, which is very close
tobr
being the upcoming v6, can be downloaded from here:br
br
a href=ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/;
target=_blankftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev//abr
br
This goes for anyone else on the list who would like to help us test v6br
prior to release.br
br
Nickbr
br
br
On Fri, 2015-05-08 at 13:36 +, Erik O#39;Hanlon wrote:br
gt; Hi Eugenio,br
gt;br
gt; That#39;s brilliant, thanks so much for the quick response. So I willbr
gt; download the v6 code and how do I call the command so that it runs thebr
gt; v6 subfield analysis from the recon_all command?br
gt;br
gt; Thanks again for the guidance. Very much appreciatedbr
gt;br
gt; Cheersbr
gt;br
gt; Erikbr
gt
Re: [Freesurfer] Hippocamp subfields
Hi Angela, It will work with subjects processed with the previous version; however, I would recommend (if possible) to run everything with the same version, for the sake of reproducibility. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 25, 2015 1:55:17 PM Subject: Re: [Freesurfer] Hippocamp subfields THank you Zeke! Do I have to repeat all the reconall command with the new freesurfer version or I can use the processed files and run only the hippo segmentation? BW Angela You can download the dev version of freesurfer which contains the new hippocampal segmentation from the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke On May 23, 2015, at 11:07 AM, angela.fav...@unipd.it wrote: Hi Bruce, I would like to test the beta version of the new hippocampal subfields segmentation function. Is it at all possible to get it and how? BW Angela yes, but the ones in V6 (which someday will make it out) are more accurate. You can get a beta and try them out if you want. cheers Bruce On Fri, 22 May 2015, Hassan bakhshi wrote: Hi, I am using freesurfer v5.3, can I have hippocamp subfields in this version?? Kind regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampal subfields
Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields
Hi FS Experts,
I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0
and I encountered the following error in the log file
Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 43: 2675 Killed ${exe_dir}/segmentSubjectT1_autoEstimateAlveusML $args
~
It appears that the process finished prematurely and didn't write out anything
in the mri/ dir.
Any pointers how to resolve ? Any help greatly appreciated
Cheers
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields
That is super Nick,
I'll download it next week and try it out. Will I need to just run the subfield
part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?
Thanks again for all the help
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH
[ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
This goes for anyone else on the list who would like to help us test v6
prior to release.
Nick
On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
Hi Eugenio,
That's brilliant, thanks so much for the quick response. So I will
download the v6 code and how do I call the command so that it runs the
v6 subfield analysis from the recon_all command?
Thanks again for the guidance. Very much appreciated
Cheers
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]
Sent: 08 May 2015 13:16
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi Erik,
the 6.0 subfield code won't overwrite your 5.3 results, so if you run
the 6.0 module on data analyzed with 5.3, both results will co-exist
in the MRI directory of each subject.
Kind regards,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon erikohan...@rcsi.ie
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 8, 2015 2:07:18 PM
Subject: [Freesurfer] hippocampal subfields
Hi FS experts,
I completed an analysis including the hippocampal subfield options
using 5.3.0. I understand that the subfield options was then removed
and I noticed that the new rev of the subfield code will be ready for
the v6 FS update. Can I use this code with my 5.3.0 code and if so
what files /dirs will I have to remove and how can I run or rerun it
to get the new subfield measures if it's possible. I would really like
to obtain the subfield measures and am not sure if I can use the
existing measures based on the 5.3.0 code. Any advice would be very
much appreciated.
Kind regards and thanks in advance
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: recon-all -s -hippo-subfields. But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command less aseg.stats gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm recon-all -s Pat2 \ -i path_to_dicoms/9-2-1.dcm and so on (2) recon-all -s subjid -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio are Pat1 and Pat2 etc... different patients? If so, they need to be run separately. e.g. recon-all -s Pat1 -i path to dicoms for patient 1) -all recon-all -s Pat2 -i path to dicoms for patient 2) -all . . . cheers Bruce p.s. for the tcsh bug you should just get your sysadmin to update the version
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi again, - Yes, if you want the whole hippocampal volumes, you can just add all the substructures. - If you compare such volumes with those from aseg.stats, you'll see that they are 10%-15% smaller, but very highly correlated. We have observed that the addition of the 5.3 subfields is a tiny bit better when it comes to separating AD from controls based solely on hippocampal volume, though. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 11:03:04 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hola Eugenio! Thank you so much for quick answer. Well telling from your response it seems that the right way to proceed in order to achieve the absolute volume is to sum up ALL given regions right? And could you please also tell me, which of the hippocampal volumes is the most correct one, the one given primarily by the recon-all or the segmented one? Thank you in advance! Best regards; Cecilio. 2015-05-21 16:54 GMT+08:00 Eugenio Iglesias e.igles...@bcbl.eu : Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: recon-all -s -hippo-subfields. But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command less aseg.stats gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : no, you need to run each subject separately. What I was saying is that you don't need
Re: [Freesurfer] Segmentation of hippocampal subfields / version 6.0 release date
Hi Josh, the module is already in the development version of FS, and will be released along with FS6 hopefully very soon. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Josh Gray jgray7...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 11, 2015 1:33:32 PM Subject: [Freesurfer] Segmentation of hippocampal subfields / version 6.0 release date Hello, I wanted to inquire about when you think that this new package for freesurfer 6.0 will be complete? I am interested in pursuing hippocampal segmentation, but it seems that I should not use the segmentation from your older program and I should wait, would you agree? Thank you, Josh -- Josh Gray Graduate Student Psychology Dept. - Clinical Program Experimental Clinical Psychopharmacology Laboratory University of Georgia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampal subfields
Hi again, FS6 is not out yet, but hopefully soon. The instructions for the new hippocampal subfield module are here: http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Erik O'Hanlon erikohan...@rcsi.ie To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 3:36:21 PM Subject: Re: [Freesurfer] hippocampal subfields Hi Eugenio, That's brilliant, thanks so much for the quick response. So I will download the v6 code and how do I call the command so that it runs the v6 subfield analysis from the recon_all command? Thanks again for the guidance. Very much appreciated Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 08 May 2015 13:16 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields Hi Erik, the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 module on data analyzed with 5.3, both results will co-exist in the MRI directory of each subject. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Erik O'Hanlon erikohan...@rcsi.ie To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 2:07:18 PM Subject: [Freesurfer] hippocampal subfields Hi FS experts, I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my 5.3.0 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the 5.3.0 code. Any advice would be very much appreciated. Kind regards and thanks in advance Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippocampal subfields
Hi once more, there is no specific longitudinal subfield module, BUT you can run the subfield code on the longitudinally processed subjects (i.e., those with tpNid.long.templateid added to their name). Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Erik O'Hanlon erikohan...@rcsi.ie To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 3:42:26 PM Subject: Re: [Freesurfer] hippocampal subfields Hi Eugenio, Sorry, forgot to ask if I can run it with the longitudinal pipeline too? Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 08 May 2015 14:36 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields Hi Eugenio, That's brilliant, thanks so much for the quick response. So I will download the v6 code and how do I call the command so that it runs the v6 subfield analysis from the recon_all command? Thanks again for the guidance. Very much appreciated Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 08 May 2015 13:16 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields Hi Erik, the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 module on data analyzed with 5.3, both results will co-exist in the MRI directory of each subject. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Erik O'Hanlon erikohan...@rcsi.ie To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 2:07:18 PM Subject: [Freesurfer] hippocampal subfields Hi FS experts, I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my 5.3.0 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the 5.3.0 code. Any advice would be very much appreciated. Kind regards and thanks in advance Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampal subfields
Hi Erik, the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 module on data analyzed with 5.3, both results will co-exist in the MRI directory of each subject. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Erik O'Hanlon erikohan...@rcsi.ie To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 2:07:18 PM Subject: [Freesurfer] hippocampal subfields Hi FS experts, I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my 5.3.0 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the 5.3.0 code. Any advice would be very much appreciated. Kind regards and thanks in advance Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Volume in hippocampus and its subfields
Hi Zih-Kai, the subfield and main FreeSurfer streams are different and therefore give different results. On average, the volumes estimated by the subfield stream will be lower, but very highly correlated with those from the main FreeSurfer stream. I hope this helps! /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: 高子凱 clandestine1...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, January 16, 2015 5:24:40 AM Subject: [Freesurfer] Volume in hippocampus and its subfields Dear All, I recently begin to use the latest FreeSurfer version to segment subcortical and hippocampus subfields in human brain of MR image. The result shows left hippocampus volume is 4332.6 mm^3 and volumeInVoxels of hippocampus subfields as below: Left-Hippocampus: 3017.11 left_presubiculum: 4103.92 left_CA1: 2247.6 left_CA2_3: 6919.65 left_fimbria: 597.982 left_subiculum: 5209.91 left_CA4_DG: 3914.19 left_hippocampal_fissure: 327.23 After I sum of the voxels and divided it by 8 ( each voxel is of the size 0.5x0.5x0.5mm^3 ), the result (3929.199 mm^3) is not equal to the hippocampus volume (4332.6 mm^3). I am quite confused how to do so. It would be great if you could advice me. Thanks a lot for your help. I really appreciate it. Beat Regard, ZK -- Zih-Kai Kao Clinical Research Assistant Psychiatry Department of Taipei Veterans General Hospital No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, Taiwan 11217, R.O.C. tel:+886-2-28712121#2912 fax:+886-2-28742421 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfields
Dear Erik / Angela, the atlas in 5.3 was derived from manual annotations on in vivo images that relied largely on geometric rules, and led to volume estimates that did not agree well with histology studies. The new atlas is based on ex vivo MRI and agrees better with histology. Moreover, it also has the option to input higher resolution images (in addition to the standard 1 mm T1), which yield a much better fit of the internal structure of the hippocampus. That said, IMHO you can still publish papers with the old tool; you just need to be careful with the interpretation of the results, and discuss these issues in the submission. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Erik O'Hanlon erikohan...@rcsi.ie To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 2, 2014 11:20:35 PM Subject: Re: [Freesurfer] Hippocampal subfields Hi FS experts, Yes, I'm in the same position and have been trying to do it longitudinally. Does this mean that the outputs are completely unreliable and unstable? Should it be parked until the release of version 6? Thanks Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of angela.fav...@unipd.it [angela.fav...@unipd.it] Sent: 02 December 2014 21:53 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields Hi all, this is really a terrible news! I am writing a paper using hippocampal subfields (ver 5.3). What is the problem with segmentation using this tool? Is it reliable at least on some of the subfield? When will Freesurfer 6 be released? Thank you Angela Hi Georg, we will be releasing with FreeSurfer 6 a new hippocampal subfield module based on a more accurate atlas built upon ex vivo MRI scans. However, if what you are interested in is the whole hippocampal volume, the results from the new module won't be too different. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Georg Ferdinand Anto von Polier gvonpol...@ukaachen.de To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 2, 2014 2:46:40 PM Subject: [Freesurfer] Hippocampal subfields Dear FreeSurfers, I am just finishing a paper using output from Hippocampal subfields and recognized that the current version has been deprecated. I am interested in volumes of the whole hippocampus. Are these volumes still valid and can you estimate when a new version will be available? Can you provide maybe a brief comment on the decision to deprecate the current version? Best regards, Georg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfields
Hi Andreia, Nothing will prevent you from running FS6's hippocampal subfields on 5.3-processed subjects, even though I'd recommend processing everything with the same version for the sake of reproducibility. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: andreia _andre...@sapo.pt To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, Eugenio Iglesias e.igles...@bcbl.eu Sent: Wednesday, December 3, 2014 2:40:33 PM Subject: Re: [Freesurfer] Hippocampal subfields Hi, Will it be possible to incorporate the new hippo subfields atlas and stats generation in the 5.3 recon-all without having to process everything from scratch with 6.0? Thank you, Andreia Citando Eugenio Iglesias e.igles...@bcbl.eu : Dear Erik / Angela, the atlas in 5.3 was derived from manual annotations on in vivo images that relied largely on geometric rules, and led to volume estimates that did not agree well with histology studies. The new atlas is based on ex vivo MRI and agrees better with histology. Moreover, it also has the option to input higher resolution images (in addition to the standard 1 mm T1), which yield a much better fit of the internal structure of the hippocampus. That said, IMHO you can still publish papers with the old tool; you just need to be careful with the interpretation of the results, and discuss these issues in the submission. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Erik O'Hanlon erikohan...@rcsi.ie To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 2, 2014 11:20:35 PM Subject: Re: [Freesurfer] Hippocampal subfields Hi FS experts, Yes, I'm in the same position and have been trying to do it longitudinally. Does this mean that the outputs are completely unreliable and unstable? Should it be parked until the release of version 6? Thanks Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu ] on behalf of angela.fav...@unipd.it [ angela.fav...@unipd.it ] Sent: 02 December 2014 21:53 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields Hi all, this is really a terrible news! I am writing a paper using hippocampal subfields (ver 5.3). What is the problem with segmentation using this tool? Is it reliable at least on some of the subfield? When will Freesurfer 6 be released? Thank you Angela Hi Georg, we will be releasing with FreeSurfer 6 a new hippocampal subfield module based on a more accurate atlas built upon ex vivo MRI scans. However, if what you are interested in is the whole hippocampal volume, the results from the new module won't be too different. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Georg Ferdinand Anto von Polier gvonpol...@ukaachen.de To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 2, 2014 2:46:40 PM Subject: [Freesurfer] Hippocampal subfields Dear FreeSurfers, I am just finishing a paper using output from Hippocampal subfields and recognized that the current version has been deprecated. I am interested in volumes of the whole hippocampus. Are these volumes still valid and can you estimate when a new version will be available? Can you provide maybe a brief comment on the decision to deprecate the current version? Best regards, Georg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list
Re: [Freesurfer] Hippocampal subfields
Hi Georg, we will be releasing with FreeSurfer 6 a new hippocampal subfield module based on a more accurate atlas built upon ex vivo MRI scans. However, if what you are interested in is the whole hippocampal volume, the results from the new module won't be too different. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Georg Ferdinand Anto von Polier gvonpol...@ukaachen.de To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 2, 2014 2:46:40 PM Subject: [Freesurfer] Hippocampal subfields Dear FreeSurfers, I am just finishing a paper using output from Hippocampal subfields and recognized that the current version has been deprecated. I am interested in volumes of the whole hippocampus. Are these volumes still valid and can you estimate when a new version will be available? Can you provide maybe a brief comment on the decision to deprecate the current version? Best regards, Georg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Number of slices generated in the brainmask.mgz
Hi Gunjan, if what you're trying to do is to bring brainmask.mgz to the native voxel space of your input scan, you can run mri_convert brainmask.mgz brainmaskResampled.nii.gz -rl input.nii.gz where input.nii.gz is the scan you fed to FreeSurfer's recon-all (e.g., recon-all -i input.nii.gz -s ) Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Gunjan Gautam gunjan.gemin...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 1, 2014 2:23:12 PM Subject: [Freesurfer] Number of slices generated in the brainmask.mgz Hi FreeSurfers, brainmask.mgz is generating 256 slides per volume. How can I have control over it, in terms of generating less number of slides (say 181) per volume? Gunjan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Amygdala subfields
Hi Stefano, we are working on an algorithm to segment the nuclei, but unfortunately I do not think it is going to be released any time soon. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: std...@virgilio.it To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 24, 2014 3:42:05 AM Subject: [Freesurfer] Amygdala subfields Dear all, is the amygdala subfields segmentation available or you are working on it? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Longitudinal analysis and hippocampal subfields
Hi Erik, did you experience the same problem with any other cases? Also, do you think you could send us the log file [subjectdir]/scripts/hippo-subfields.log, as well as the contents of [subjectdir]/tmp/subrieldResults? Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Erik O'Hanlon erikohan...@rcsi.ie To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 20, 2014 2:04:15 PM Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Martin, I appear to have run into an issue when processing longitudinal data with the -hippo-subfields command. I get the following error. I have run the process in the cross (independent) mode and it ran okay at each time point (I have two). Wrote out aseg_thresholded.mgz kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 imageFileName: aseg_thresholded.mgz radius: 3 Using dilating filter itk::ExceptionObject (0x2ccf4d0) Location: void itk::ImageFileWriterTInputImage::Write() [with TInputImage = main(int, char**)::ImageType] File: /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileWriter.txx Line: 271 Description: itk::ERROR: ImageFileWriter(0x2cb8880): Largest possible region does not fully contain requested paste IO regionPaste$ Dimension: 3 Index: 0 0 0 Size: 0 0 0 Largest possible region: ImageRegion (0x7fff9c9b02e0) Dimension: 3 Index: [0, 0, 0] Size: [0, 0, 0] failed to do kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 Linux tcin-n08.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub040_tp1.long.sub040_T1_baseimage exited with ERRORS at Wed Nov 19 20:34:12 GMT 2014 For more details, see the log file /projects/pi-frodlt/HPC_11_00383/Freesurfer_ABD/sub040_tp1.long.sub040_T1_baseimage$ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas very much appreciated. Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 18 November 2014 20:42 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields That's super! Thanks again Martin Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 18:07 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu ] on behalf of Martin Reuter [ mreu...@nmr.mgh.harvard.edu ] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu
Re: [Freesurfer] Freeview-stable4 error?
Thanks! Unfortunately it won't help; I need specific versions with specific compilation options etc :-( Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Stephanie N. DeCross sdecr...@mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: Wednesday, November 5, 2014 10:33:54 AM Subject: [Freesurfer] Freeview-stable4 error? Hi, I'm trying to look at 2 connectivity files (saved in SPM) at the same time using Freeview, but how I've been doing it in the past is no longer working and I haven’t changed anything on my end. What I had been doing: 1. cd to the folder with my connectivity files and typing the shortcut command: stable4 (which does the following: setenv USE_STABLE_4_5_0; source /space/freesurfer/nmr-stable4-env) 2. typing the command: freeview ../../../../N12Trio_avg152T1.nii LSHSxAmyg.covBDI_PosCorr_p05_20vox.img LSHSxAmyg.covBDI_NegCorr_p05_20vox.img_blue.nii.gz This command used to work fine, but is now giving me the error: freeview.bin: error while loading shared libraries: libvtkverdict.so.vtk5.2.0: cannot open shared object file: No such file or directory This command DOES work if I don't type the shortcut command stable4 and instead keep using the stable53 environment I was already in (setenv FSL_DIR /usr/pubsw/packages/fsl/4.1.9; source /space/nexus/1/users/avi-tools/enable_avi.csh; setenv SUBJECTS_DIR /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53; source /usr/local/freesurfer/nmr-stable53-env). While I'm not positive it affects anything, I'd rather be consistent with the stable4 way I've been doing it in the past - is there a way to fix it and use Freeview in stable4, or does this freeview.bin error mean that I can no longer use Freeview with stable4? Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampal subfields: from posterior to binary masks
Hi again, Luigi, this sentence that you wrote summarizes everything pretty well: I think that the posterior files outputted by freesurfer are missing the final step of required to each voxel to the single label with the highest posterior prob. We will implement this in the next FS release. Regarding how the discrete labels are computed: For each voxel, one would look at all the posterior probabilities, and assign the label corresponding to the largest posterior. There is a small chance that there is a tie between 2 (or more) classes; in that case, you can pick between those classes at random. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Luigi Antelmi luigi.ante...@gmail.com To: e iglesias e.igles...@bcbl.eu, freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 9, 2014 11:48:10 AM Subject: Re: [Freesurfer] hippocampal subfields: from posterior to binary masks Dear Eugenio, assign to each voxel the label with the highest posterior probability implies that each voxel must belong to one and only one label, right? I've found that this is not the case with the posterior_*.mgz files outputted by freesurfer, where each voxel (especially the ones with the lower prob values) can belong to multiple labels. The passages I've done to come up at this conclusion was: 1) binarize all the posterior maps 2) summing them up 3) search for values greater than 1 4) if there are values 1, then there are voxels belonging to multiple labels. I've found voxels belonging to 7 different labels at the same time! I think that the posterior files outputted by freesurfer are missing the final step of required to each voxel to the single label with the highest posterior prob. I think that a clarification from the developers is needed here. Best regards, Luigi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippocampal subfields: from posterior to binary masks
Dear Luigi, the MAP solution (which maximizes the posterior probability of the segmentation given the image and the atlas) is to assign to each voxel the label with the highest posterior probability. The expected value of the volume of a structure is indeed the integral of the its posterior across the image - which can be very different from the volume stemming from counting the voxels in the discrete MAP segmentation. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Luigi Antelmi luigi.ante...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Cc: Jorge Jovicich jorge.jovic...@unitn.it, Moira Marizzoni mmarizz...@fatebenefratelli.it Sent: Monday, September 8, 2014 3:57:38 PM Subject: Re: [Freesurfer] hippocampal subfields: from posterior to binary masks Dear all, I just found that the equivalence Volume/integral isn't quite correct. The equivalence must be between the volume and something like an expected value of the histogram V = E[H] = ∫xH(x) dx (where x is the greyscale value). So, the point 2) described in my previous email becomes (with some intermediate passages) Find the threshold value thr such that: Does this make any sense to you? Luigi. 2014-09-08 9:49 GMT+02:00 Luigi Antelmi luigi.ante...@gmail.com : Dear list members, as you know, the hippocampal subfields given back by FreeSurfer (posterior_left_CA1.mgz, posterior_left_CA2-3.mgz, etc.) are posterior probability maps in the range [0-255] (i.e. [0-1] with 8 bit of quantization). Although there is a way to calculate the volume ( kvlQuantifyPosteriorProbabilityImages ) that operates by summing up all the greyscale values (an equivalent method is to integrate the histogram over the range 0-255), to my knowledge there is no freesurfer's routine able to extract a binary mask out of the posterior probability map. What procedure do you use or suggest? I think there are two possibilities here. 1) As written in the paper from Van Leeput et al. , I can assign each voxel to the label with the highest posterior probability . Althought I'm wondering why such a thing, documented in the paper, has not been implemented yet, I do not think this is the right way to do it because this procedure do not make any distinction between low probability voxels and high prob ones. 2) Threshold the subfields such that the volumes of the thresholded mask will equal those calculated by integrating the histogram on the domain 0-255; Formally, find t such that: where H is the histogram of the subfield. I prefer the second option because here low prob values are discarded, and because one can apply the equation to a rigid transformed subfield, thus limiting the partial volume effect of the resampling. What do you think about? Luigi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal Subfields missing nonPartialVolumeStatsRight.txt file
Hi Yoon, when you run the script kvlQuantifyHippocampalSubfieldSegmentations.sh, it goes along the volumeStats_left.txt and volumeStats_right.txt to build a large table with all the volumes. The output files (nonPartialVolumeStatsLeft.txt/nonPartialVolumeStatsRight.txt) should be in your subjects directory $subject. Regarding the partial volume segmentation, it's not fully implemented / tested yet. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Yoonho Chung yoonho.ch...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 15, 2014 10:33:19 PM Subject: [Freesurfer] Hippocampal Subfields missing nonPartialVolumeStatsRight.txt file Hi, I am running Hippocampal subfield processing stream and I think I got all the appropriate posterior_*.mgz files I need to get the stats, but I am not seeing nonPartialVolumeStatsRight.txt anywhere as described in the wiki under $subjectsdir. What I am seeing is volumeStats_left.txt and volumeStats_right.txt files under the $subject/mri directory and one of the text files look like this. volumeInVoxels: Left-Hippocampus: 2616.97 left_presubiculum: 4050 left_CA1: 2880.55 left_CA2_3: 8120.59 left_fimbria: 212.439 left_subiculum: 5985.02 left_CA4_DG: 4459.07 left_hippocampal_fissure: 358.59 - If I look at the end of the hippo-subfields.log file, it is saying it is skipping the partial volume segmentation (see below). --- ... Debug: Off Observers: none Matrix: -0.5 0 0 0 0 0.5 0 -0.5 0 Offset: [41.7047, -40.8148, -4.10007] Center: [0, 0, 0] Translation: [41.7047, -40.8148, -4.10007] Inverse: -2 0 0 0 0 -2 0 2 0 Singular: 0 spacing: [0.5, 0.5, 0.5] origin: [41.7047, -40.8148, -4.10007] direction: -1 0 0 0 0 1 0 -1 0 done! Skipping the partial volume segmentation part --- Can please someone tell me what I am missing? Also, what do I need to do to extract the values to a spreadsheet? Should I use asegstats2table? under '-help' it doesn't say which options it should be used to get the subfields. Thank you so much for the help in advance. Cheers, Yoon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] -hippo-subfields
Hi Greg, I would suggest that you only do it with either autorecon2 or autorecon3. With autorecon1, it will fail because it won't find aseg.mgz. You should still be able to run autorecon2 after this mistake, but I wouldn't do it (why let the software exit with an error without need?). If you do it both with both autorecon2 and autorecon3, I believe that the code will be run twice. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Gregory Kirk gk...@wisc.edu To: free freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 7, 2014 5:05:27 PM Subject: [Freesurfer] -hippo-subfields we have freesurfer set up on our big condor cluster, i asked that the -hippo-subfields be added. they have it set up to run in 3 stages autorecon1 autorecon2 autorecon3 they added the flag to all 3, i think it would only be needed on autorecon3, but don't think it would cause harm, just be ignored in the first 2 ? thanks greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ?Sequence for Hippo_subfields
Hi Kev, 1. It will able to use only the T1, only the T2, or both simultaneously. 2. The algorithm is relatively robust against these parameters. However, the higher the resolution and the lower the noise the better (as usual). Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Schumman schumm...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 16, 2014 6:47:21 PM Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields Dear Eugenio, I'm following up on this thread. After some discussion with the radiologist, some relevant questions have come up: 1. Is Freesurfer going to make use of both the T1 and the T2 sequences in the processing stream of hippocampal subfields? 2. If the answer is yes how important is that the T1 weighted and the T2 sequences are similar in terms on slice thickness (eg. both 1mm ISO), FOV, and other parameters? Thanks, Kev On 2014-06-12, at 12:36 PM, Eugenio Iglesias wrote: Yes! If Im not mistaken, ADNI is acquiring this type of data on 3T platforms. Cheers Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thu, 12 Jun 2014 18:51:03 +0200 (CEST) Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields Much appreciated Eugenio. I had read a paper where authors report using a ultra high field scanner (7T - Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference you kindly provided uses a 4T scanner... I presume using a 3T might be stretching things a bit, and I wonder whether future FS releases using T2-weighted images will accept 3T scans? Best regards and thanks again for great support you guys provide, Kev On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote: Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [Freesurfer] ?Sequence for Hippo_subfields Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal Subsectioning
Hi Joshua, the measurements are in voxels, so you need to multiply them by 0.125 (which is 0.5^3) to obtain values in mm3. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Joshua S nitrosomonas...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 11, 2014 5:46:59 PM Subject: [Freesurfer] Hippocampal Subsectioning Hi, I was doing a hippocampal subsectioning on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Linear Mixed Models in FS?
Ey! Dice Lilla que estas currando en el Childrens? Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: jorge luis jbernal0...@yahoo.es To: Lars M. Rimol lari...@gmail.com Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 19, 2014 8:56:38 AM Subject: Re: [Freesurfer] Linear Mixed Models in FS? Yes there is numerical instability when p-values becomes extremely low and y our solution is OK. You are just being conservative. Your actual p-value might have been 1e-25 but you couldn't observe it exactly (got zero instead) because of numerical limitations of the Matlab's fcdf function. I'll fix this issue on github: https://github.com/NeuroStats this weekend. Best -Jorge De: Lars M. Rimol lari...@gmail.com Para: jorge luis jbernal0...@yahoo.es CC: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Enviado: Jueves 19 de junio de 2014 5:01 Asunto: Re: [Freesurfer] Linear Mixed Models in FS? Hi Jorge, Thank you! Yes this makes sense, because this confirms that the second covariate in fact tests for an effect across all groups, just as I expected. Now, there's another problem with these analyses: Please consider the attached figure lh_model1_01000_interaction_nopatch_lateral.tif , which shows a p-map (cortical area, smoothed with 30 mm fwhm) with two gray regions in the temporal lobe and the insula/IFG in the middle of highly significant regions. There is no darker blue transition into the non-significant regions. These gray regions appear to be artifacts based on eye balling of the maps. I checked the output of the significance testing in those regions and it appears that the output of this formula (in lme_mass_f.m) is extremely low: pval(i) = 1-fcdf(Fstat,szC,m); I assume there may be numerical instability when pval becomes extremely low? Could that explain this? I changed the code so that if 1-fcdf(Fstat,szC,m) is zero or less than 1e-15, then pval(i) = max(1-fcdf(Fstat,szC,m),1e-15); (or, if it's negative pval(i) = min(1-fcdf(Fstat,szC,m),-1e-15) ) If it's not, then the old code applies: pval(i) = 1-fcdf(Fstat,szC,m); This seems to have fixed the problem as the figure model1_area_lh_01000_winteraction_wpatch_lateral.tif shows. Again, based on eye-balling the maps. I have seen this problem in several data sets, both cortical and subcortical data. In all cases using a lower limit for 1-fcdf(Fstat,szC,m) - either 1e-15 or 1e-20 - seems to fix the problem. Do you concur that the problem is numerical instability and is this a good way to fix it? Thank you! yours, LMR On Wed, Jun 18, 2014 at 3:49 PM, jorge luis jbernal0...@yahoo.es wrote: Hi LMR If the interaction term is not statistically significant then there is no evidence of the existence of two different groups in your sample (as far as the longitudinal trajectory is concerned they are all controls, the groups might be different at baseline though). This is why main effects are only tested after the interactions have been previously tested. In your model a common “base time slope” is assumed for both groups (the second coefficient) but you are also explicitly modeling the possibility of the case-group slope being exceeding the control/common base slope by an extra quantity. That quantity is the interaction term. Hope this makes sense Best -Jorge De: Lars M. Rimol lari...@gmail.com Para: FS maling list freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 18 de junio de 2014 8:57 Asunto: Re: [Freesurfer] Linear Mixed Models in FS? Hi Jorge, Thank you for your reply! Again considering the same model from before intercept(random effect) + centered age + group + group x centered age + sex I think what is confusing me is that I think of the [centered age] covariate as a column vector which will contain the centered age of both the control- and the case group. This is how it would be seen in a GLM using the same design matrix. Therefore it is difficult for me to understand how the contrast [0 1 0 0 0] can inform us about the control group alone. To me it would seem obvious that this contrast tells me something about the effect of [centered age] on the whole of the sample, regardless of the group each subject belongs to. On the other hand, I agree with you that the interaction term could tell us something about the effect of [centered age] on the case-group by considering the contrast vector [0 0 0 1 0]. Just for the sake of argument, please consider the following model intercept(random effect) + (1-group) x centered age + group + group x centered age + sex and compare to the one presented above. Here (1-group) is a column vector which is 1 where the [group] vector is 0, and vice versa. This difference ensures that the second term only
Re: [Freesurfer] ?Sequence for Hippo_subfields
Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [Freesurfer] ?Sequence for Hippo_subfields Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ?Sequence for Hippo_subfields
Yes! If Im not mistaken, ADNI is acquiring this type of data on 3T platforms. Cheers Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thu, 12 Jun 2014 18:51:03 +0200 (CEST) Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields Much appreciated Eugenio. I had read a paper where authors report using a ultra high field scanner (7T - Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference you kindly provided uses a 4T scanner... I presume using a 3T might be stretching things a bit, and I wonder whether future FS releases using T2-weighted images will accept 3T scans? Best regards and thanks again for great support you guys provide, Kev On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote: Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [Freesurfer] ?Sequence for Hippo_subfields Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] kvlQuantify naming problem [possible fix]
Thank you very much! We'll certainly fix this in the next release Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: C.P. Frost cpfr...@wisc.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 21, 2014 9:58:32 PM Subject: Re: [Freesurfer] kvlQuantify naming problem [possible fix] Follow-up: I then run into indexing problems when calling freeview with subfield volumes (similar to http://bit.ly/1pdEWRZ ), which leads me to believe kvlQuantify is the only script that relies on the old convention. Changing the names back to CA2_3.mgz, etc., fixes THAT problem. Rather than changing the filenames to the old convention, it's probably better to fix the script and leave the filenames alone. On Wed, May 21, 2014 at 1:06 PM, C.P. Frost car...@gmail.com wrote: Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem ( http://bit.ly/1vHbV5K ), so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla
Hi Josh, the method fits a statistical atlas of the hippocampal subfields to the image data. It is assumed that all subfields other than the fimbria have the same distribution of intensities - because they are all assumed to be gray matter. Therefore, most of the internal boundaries of the hippocampus rely on the prior given by the deformed atlas, which is mostly determined by the global hippocampal shape. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Joshua Lee jki...@ucdavis.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 1, 2014 8:03:04 PM Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla Thanks for the clarification Eugenio. Would saying that it relies on shape instead of surface be more accurate? I would like to understand better. Also, it is good news that there are plans to model the SLRM. Josh - Joshua Lee Doctoral Candidate Department of Psychology Center for Mind and Brain University of California, Davis 530.747.3805 On Mon, Apr 28, 2014 at 12:18 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote: Dear all, the current module in FreeSurfer works with 1mm T1 data, by relying on strong shape priors. So, at this point, feeding the algorithm data from a 3T scanner or a 1.5T scanner is pretty much the same. Joshua, it is indeed inaccurate to say that the method relies on a generated hippocampal surface, but you are definitely right regarding the SLRM: it is not modeled at this point (we have a new version that models it coming out hopefully soon!). Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Joshua Lee jki...@ucdavis.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, April 25, 2014 2:10:29 AM Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla Hi Alan, Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x 0.4 mm in-plane resolution). The thickness of a CA subfield typically range between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter resolutions. Further, subfield segmentation typically requires high-contrast data to discern the internal boundaries formed by the stratum radiatum/stratum lacunosum-moleculare (SLRM). I doubt that images produced on a 1.5 T magnet can achieve the necessary contrast. Last, and please someone correct me if what I say is inaccurate, but doesn't the Van Leemput method use statistical priors to apply label probabilities in reference to a generated hippocampal surface? This would imply that the method assigns label probabilities without reference to a subject's SLRM intensity information. For volumetry, I am somewhat skeptical that a method that only relies on a generated surface would be sensitive to group x subfield interactions; especially double dissociations in ! which overall volume/shape of the hippocampus may be similar across groups. That the that was generated from potentially low resolution, low contrast data cannot help the matter. Some may disagree about this though and I'd be interested in hearing what other people think about the matter. In general, I am quite optimistic about automated methods to segment the subfields. Joshua - Joshua K. Lee Doctoral Candidate Department of Psychology Center for Mind and Brain University of California, Davis On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis alandarkene...@gmail.com wrote: Hi Bruce and FreeSurfers: I have received a manuscript to review for possible publication. The authors have used the subfields algorithm on 1.5T scans and obtained a parcellation with values. They have drawn some major conclusions on the basis of the findings. My understanding is that this method can only be done on 3T. Is the 1.5T results valid? Please advice. thanks, Alan Francis ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only
Re: [Freesurfer] FS volume discrepancies
Dear Petr, the volumes from the subfields are in voxels. Since the voxels are 0.5mm isotropic, their volumes is (1/8) cubic millimeters. Therefore, you need to divide the volumes by 8 to convert to mm3. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: zach petr zach.p...@post.cz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 15, 2014 4:05:43 PM Subject: Re: [Freesurfer] FS volume discrepancies Thanks for reply. But adding subfield volumes together leads to too high number compared to overall hippocampus volume. Like 9500 mm3 compared to 2.1 mm3. Petr -- Původní zpráva -- Od: Bruce Fischl fis...@nmr.mgh.harvard.edu Komu: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Datum: 15. 4. 2014 14:35:13 Předmět: Re: [Freesurfer] FS volume discrepancies From Eugenio: Dear Petr, at this point, the hippocampal subfield module is - to some extent - independent from the whole hippocampal segmentation. The values you will obtain from adding the subfield volumes together will be around 15% lower than the volumes from aseg.stat, but they will still be very highly correlated. Kind regards, On Tue, 15 Apr 2014, zach.p...@post.cz wrote: I have several issues concerning automated volumes calculation. When you look at the aseg.stat for hippocampal volume (in mm3) it gives different value compared to hippocampal subfields volume calculation (which comes in voxels but there is stated that 1 voxel is 0.5mm3). How is it possible? I presume that anatomical definition and subfield incorporation is the same. Next - if you look at the whole hippocampal formation volume in hippocampal subfield calculations it is way lower compared to the summation of the CA1-CA4 + dentate gyrus = hippocampal formation. What could be explanation of this? Petr ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
