Re: [Freesurfer] beta
Hi Colin, actually there is no hard limit for the size of your input data, except for the subcortical segmentation which behaves quite strange. What I currently do is to run recon-all on the hires data normally conforming the data. Then I use the upsampled brainmask as a mask to skullstrip my hires data and the upsampled aseg stuff to feed the upcoming stages of the recon-all pipeline. The -fix stage takes incredibly long that is why I'm trying to find a suitable work-around here. All other stages are being run normally. Although isotropic data and the -noconform flag are mandatory. Best, Falk Original-Nachricht Datum: Mon, 21 Jan 2013 19:19:25 -0500 (EST) Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Colin Reveley reve...@gmail.com CC: Joshua Lee jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu, Nick Schmansky ni...@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] beta Hi Colin yes, but we simply don't have the person power to do it at the moment. Our FS support grant ends in a month and is not going to get renewed, so it's going to be hard to do anytime soon. sorry Bruce On Mon, 21 Jan 2013, Colin Reveley wrote: do you plan to support data that is more that 256^3, ever? just, do you plan to support that On 21 January 2013 22:17, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, it won't change anything on the subcortical side yet On Mon, 21 Jan 2013, Joshua Lee wrote: Thanks Bruce. That sounds great. Will subcortical segmentations also benefit yet. I remember that you once told me that there were some problems with it. - Josh On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Josh the way we are handling sub-mm data is to run it through the standard recon-all, then run a postprocessing surface deformation on the higher res data. Our preliminary results are pretty encouraging on T1s, T2s and FLAIRs. cheers Bruce On Mon, 21 Jan 2013, Joshua Lee wrote: Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not be possible next version? Josh On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Colin, It will still error if any dimension is greater than 256, which then means the flag -cw256 must be added to recon-all. This flag chops dimensions greater than 256 down to 256. The reason it doesnt do it automatically is that with this chopping, its not certain that it isnt removing into the head, so the user needs to be aware of this, so that they can inspect orig.mgz with freeview to make sure the head is fully visible. Nick Does the beta permit volumes bigger than 256^3 voxels? just askingand just asking about raw dimensions in unit-voxels at the start of pipeline cheers Colin On 18 January 2013 17:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. v5.2.0 beta, round two (Nick Schmansky) 2. Re: pial not
[Freesurfer] Renaming subject directories
Dear Freesurfers, Is it ok to rename a subject directory, then run tkmedit and recon-all procedures and then rename the directory back again or will this cause problems? All the best, Anders ___ 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] Results Vary
Dear FS team, I processed two set of MRI data for a single patient,Thats BL scan and TP1.I ran both scans on a Mcbook Pro and a PC with Virtual machine installed. Though I was expecting the same segstats,the results vary from Macpro to VM.For eg , for BL in Mac SubCortGrayVol is 178038 but for the same images in VM the results are 177432.Does it happened to any one beforeWhats the reson its happening and how can I remedy,validate the results. Much appreciate your advice,... In Thanks Chikku. ___ 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] dimension mismatch: Cortical Thickness of a Volume-defined ROI
Hi Doug and other FS-experts, I succesfully applied the registration step of the Cortical Thickness of a Volume-defined ROI wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness However, I'm having troubles at the end. 3) Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface overlay. This works perfectly: (fsaverage dir) mri_vol2surf --mov ../../Parietal_Sup_L152.nii --reg ../../test.register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fs.average.parietal.mgh --reshape Then viewing: tksurfer fsaverage lh inflated -overlay lh.fsaverage.parietal.mgh -fthresh 0.5 Is also perfect. The problem arises in step 4/5. First: 4) Map your subject thickness data to the fsaverage subject. Do this for all your subjects. mri_surf2surf --s BT1P0392_9_1 --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape srcsubject = BT1P0392_9_1 srcval = lh.thickness srctype= trgsubject = fsaverage trgval = lh.thickness.fsaverage.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//BT1P0392_9_1/surf/lh .sphere.reg Loading source data Reading target surface reg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//fsaverage/surf/lh.sp here.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (144750) Reverse Loop had 31554 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 141619, nTrgMulti = 3, MnTrgMultiHits = 2.41988 nSrc121 = 107010, nSrcLost = 0, nSrcMulti = 37740, MnSrcMultiHits = 2.34197 Saving target data Reshaping 6 (nvertices = 163842) Saving to lh.thickness.fsaverage.mgh Here all is well. But then: 5) Run mri_segstats, using the subject-ROI surface, to get the thickness data for your ROI. mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt sysname Linux hostname corleone01univ.nl machine x86_64 user cedric Loading /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 If I then follow the suggestion to use the --reshape-factor 7 and re-run steps 4 and 5, I keep on getting the same error message ERROR: dimension mismatch between input volume and seg. Do you have any ideas what is going (wr)on(g)? Many thanks, Cédric ___ 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] qdec
Hi, I am considering using qdec, however due to our large dataset (and different individuals having been in charge at different times) I just realized that the folders fsaverage etc are missing. As these are necessary for the qdec use, is there anything else I can do? Eg a command line to just generate the fsaverage for all my subjects? Thank you for your help -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Two questions: autocorrelation correction and vertex distance
On 01/19/2013 03:18 PM, Alex Kell wrote: Hi Freesurfers, I have two unrelated questions. 1. I want to pre-whiten some functional data without running a GLM on them (we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and mailing archives, but I can't find how to pre-whiten the data without running a GLM. Is there a straightforward way? If not, I guess we could just do it in matlab. FSFAST uses an AR1 model. It computes the AR1 from the residuals (thus needing to run the GLM first). The voxel-wise AR1 is spatially smoothed, then binned into 10 bins. All the voxels in each bin are then analyzed in the same way. 2. Separately, we're bringing some volume masks to the surface and are preprocessing them with dilation and erosion to clean them up. We're trying to get a sense of how much is a reasonable amount to dilate and erode by, and it would be helpful to know about how far apart the adjacent surface vertices are. Roughly, what's the mean distance between adjacent vertices? About 1mm doug Thanks in advance. Best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Citation for mri_glmfit-sim
Cite Donald Hagler's 2006 paper in NI. doug On 01/20/2013 01:06 PM, Shantanu Ghosh wrote: Hi Freesurfers, Can you point out the correct paper that I can cite for the clusterwise correction for multiple comparisons computed by mri_glmfit-sim in v5.0 ? Thanks, Shantanu -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Renaming subject directories
no, it should not cause problems. doug On 01/22/2013 07:47 AM, Anders Hougaard wrote: Dear Freesurfers, Is it ok to rename a subject directory, then run tkmedit and recon-all procedures and then rename the directory back again or will this cause problems? All the best, Anders ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Results Vary
Hi Chikku, while we try to resolve these differences, you are not guaranteed to get identical results when you use different platforms. This is an issue with using different computes and applies to all software, not just FS.It is caused by the use of different math libraries and different binary operations. The difference you show is only 0.3% which should not be enough to cause false results. doug On 01/22/2013 08:13 AM, Varghese Chikku wrote: Dear FS team, I processed two set of MRI data for a single patient,Thats BL scan and TP1.I ran both scans on a Mcbook Pro and a PC with Virtual machine installed. Though I was expecting the same segstats,the results vary from Macpro to VM.For eg , for BL in Mac SubCortGrayVol is 178038 but for the same images in VM the results are 177432.Does it happened to any one beforeWhats the reson its happening and how can I remedy,validate the results. Much appreciate your advice,... In Thanks Chikku. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] dimension mismatch: Cortical Thickness of a Volume-defined ROI
Hi Cedric, try it with --noreshape. If you're using mgh format, then reshaping is not necessary. doug On 01/22/2013 09:16 AM, Koolschijn, Cédric wrote: Hi Doug and other FS-experts, I succesfully applied the registration step of the Cortical Thickness of a Volume-defined ROI wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness However, I'm having troubles at the end. 3) Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface overlay. This works perfectly: (fsaverage dir) mri_vol2surf --mov ../../Parietal_Sup_L152.nii --reg ../../test.register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fs.average.parietal.mgh --reshape Then viewing: tksurfer fsaverage lh inflated -overlay lh.fsaverage.parietal.mgh -fthresh 0.5 Is also perfect. The problem arises in step 4/5. First: 4) Map your subject thickness data to the fsaverage subject. Do this for all your subjects. mri_surf2surf --s BT1P0392_9_1 --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape srcsubject = BT1P0392_9_1 srcval = lh.thickness srctype= trgsubject = fsaverage trgval = lh.thickness.fsaverage.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//BT1P0392_9_1/surf/lh .sphere.reg Loading source data Reading target surface reg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//fsaverage/surf/lh.sp here.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (144750) Reverse Loop had 31554 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 141619, nTrgMulti = 3, MnTrgMultiHits = 2.41988 nSrc121 = 107010, nSrcLost = 0, nSrcMulti = 37740, MnSrcMultiHits = 2.34197 Saving target data Reshaping 6 (nvertices = 163842) Saving to lh.thickness.fsaverage.mgh Here all is well. But then: 5) Run mri_segstats, using the subject-ROI surface, to get the thickness data for your ROI. mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt sysname Linux hostname corleone01univ.nl machine x86_64 user cedric Loading /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 If I then follow the suggestion to use the --reshape-factor 7 and re-run steps 4 and 5, I keep on getting the same error message ERROR: dimension mismatch between input volume and seg. Do you have any ideas what is going (wr)on(g)? Many thanks, Cédric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] qdec
Hi Catherine, fsaverage is part of the FS distribution. You can just: cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage . This will create a symbolic link to fsaverage in your $SUBJECTS_DIR doug On 01/22/2013 09:17 AM, Catherine Bois wrote: Hi, I am considering using qdec, however due to our large dataset (and different individuals having been in charge at different times) I just realized that the folders fsaverage etc are missing. As these are necessary for the qdec use, is there anything else I can do? Eg a command line to just generate the fsaverage for all my subjects? Thank you for your help -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] (no subject)
That should not happen. Concentrating on the Mac for a moment, please send the recon-all.log files for both runs. doug On 01/22/2013 10:36 AM, Varghese Chikku wrote: Many thanks Doug, I forgot to mention,I ran same patient,same time point,twice on Mac and VM and the results varied each time.So why is it happening though I am using the same machine and same set of images. Cheers, Chikku -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Trouble with Initial Processing - Very Dark Images
Dan: just to be clear this has nothing to do with nifti vs. dicom. It's likely that your tech ran prescan normalize and the nifti is the series that was normalized. cheers Bruce On Tue, 22 Jan 2013, Dan LaFreniere wrote: Hey Falk, Much appreciated for your reply on this! Fortunately I was able to correct the issue by contacting our MRI tech - he suggested we use his nifti files instead and the results turned out a lot better. I emailed Bruce but forgot to include the freesurfer mailing list in the CC. Here is an attached screenshot of my final results with the nifti files for the record. Thanks again for the replies! I'm sure I'll be contacting the experts down the road. Cheers, Dan On Tue, Jan 22, 2013 at 4:06 AM, Falk Lüsebrink falk.lu...@gmx.net wrote: Hey Dan, Bruce might be right about the SNR, but you could try to adjust the parameters of the inhomogeneity correction in the N3 algorithm. You could either use the following command line: recon-all -autorecon1 -mprage -nuintensitycor-3t -i data -s subject Or if this still isn't good enough, try changing the parameters of the N3 manually (e.g. distance and fwhm): SUBJ=ab11 recon-all -motioncor -talairach -tal-check -i data -s $SUBJ mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.mgz --o $SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15 --fwhm 0.5 --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/transforms/talairach.xfm recon-all -mprage -normalization -skulstrip -s $SUBJ If the skullstrip looks fine continue by using this: recon-all -mprage -autorecon2 -autorecon3 -s $SUBJ Best, Falk Original-Nachricht Datum: Mon, 21 Jan 2013 22:39:29 -0500 Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Dan LaFreniere lafreniere...@gmail.com CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Trouble with Initial Processing - Very Dark Images Wow, that's a huge bias field! Control points will help uniformity, but the snr may not be good enough for good results Bruce On Jan 18, 2013, at 11:09 AM, Dan LaFreniere lafreniere...@gmail.com wrote: Hey all, I'm very new to Freesurfer and am having some issues with the initial processing of our MPRAGE dicom files. So far, I'm able to get initial -autorecon1 steps to work but once this has finished and I open my brainmask.mgz files and the brain is incredibly dark in inferior regions. So much so that the skull strip appears to be removing large chunks of anterior temporal lobes. What remains of the temporal lobes is incredibly dark with grey matter almost indistinguishable from CSF. I would really like to look into freesurfer for cortical thickness analysis of subcortical regions since it seems like such an awesome program but I have really been struggling to get a decent looking brain. It's probably noteworthy that these brains have always been quite dark but I'm usually able to correct them to a point where they're pretty good in other programs. I have read about a few solutions to the problem but am having trouble implementing them. One suggestion was to use the -mprage flag; unfortunately, I'm not sure how to run this or when. Another suggestion was to use control points but I don't yet have the red and blue segmentation boundary lines - I'm using tkmedit FoM04_KA brainmask.mgz -aux T1.mgz to view the files. For reference, this is the line I use to run autorecon1: Recon-all -autorecon1 -subjid FoM04_KA Does anyone have any suggestions as to what I could do? It would be greatly appreciated. I've attached a screenshot to illustrate. Also, we used a 4.7T Varian scanner with 0.375/0.375/1mm voxels. I believe we used a gradient echo multislice sequence. In addition, all subjects' data have been obtained so there is no chance of changing sequences? Best wishes, Dan ___ 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
Re: [Freesurfer] Trouble with Initial Processing - Very Dark Images
That was exactly what he said as well; sorry that I wasn't more clear with
my email.
Cheers guys,
Dan
On Tue, Jan 22, 2013 at 9:04 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Dan: just to be clear this has nothing to do with nifti vs. dicom. It's
likely that your tech ran prescan normalize and the nifti is the series
that was normalized.
cheers
Bruce
On Tue, 22 Jan 2013, Dan LaFreniere wrote:
Hey Falk,
Much appreciated for your reply on this! Fortunately I was able to
correct the issue by contacting our MRI tech - he suggested we use his
nifti files instead and the results turned out a lot better. I emailed
Bruce but forgot to include the freesurfer mailing list in the CC.
Here is an attached screenshot of my final results with the nifti files
for the record. Thanks again for the replies! I'm sure I'll be
contacting the experts down the road.
Cheers,
Dan
On Tue, Jan 22, 2013 at 4:06 AM, Falk Lüsebrink falk.lu...@gmx.net
wrote:
Hey Dan,
Bruce might be right about the SNR, but you could try to adjust the
parameters of the inhomogeneity correction in the N3
algorithm.
You could either use the following command line:
recon-all -autorecon1 -mprage -nuintensitycor-3t -i data -s
subject
Or if this still isn't good enough, try changing the parameters of
the N3 manually (e.g. distance and fwhm):
SUBJ=ab11
recon-all -motioncor -talairach -tal-check -i data -s $SUBJ
mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.**mgz --o
$SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15
--fwhm 0.5 --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/**
transforms/talairach.xfm
recon-all -mprage -normalization -skulstrip -s $SUBJ
If the skullstrip looks fine continue by using this:
recon-all -mprage -autorecon2 -autorecon3 -s $SUBJ
Best,
Falk
Original-Nachricht
Datum: Mon, 21 Jan 2013 22:39:29 -0500
Von: Bruce Fischl fis...@nmr.mgh.harvard.edu
An: Dan LaFreniere lafreniere...@gmail.com
CC:
freesur...@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu
freesur...@nmr.mgh.harvard.**edu freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Trouble with Initial Processing - Very
Dark Images
Wow, that's a huge bias field! Control points will help
uniformity, but
the snr may not be good enough for good results
Bruce
On Jan 18, 2013, at 11:09 AM, Dan LaFreniere
lafreniere...@gmail.com
wrote:
Hey all,
I'm very new to Freesurfer and am having some issues with the
initial
processing of our MPRAGE dicom files. So far, I'm able to get
initial
-autorecon1 steps to work but once this has finished and I open
my brainmask.mgz
files and the brain is incredibly dark in inferior regions. So
much so that
the skull strip appears to be removing large chunks of anterior
temporal
lobes. What remains of the temporal lobes is incredibly dark with
grey matter
almost indistinguishable from CSF.
I would really like to look into freesurfer for cortical
thickness
analysis of subcortical regions since it seems like such an
awesome program but
I have really been struggling to get a decent looking brain. It's
probably
noteworthy that these brains have always been quite dark but I'm
usually
able to correct them to a point where they're pretty good in
other programs.
I have read about a few solutions to the problem but am having
trouble
implementing them. One suggestion was to use the -mprage flag;
unfortunately, I'm not sure how to run this or when. Another
suggestion was to use
control points but I don't yet have the red and blue segmentation
boundary lines
- I'm using tkmedit FoM04_KA brainmask.mgz -aux T1.mgz to view
the files.
For reference, this is the line I use to run autorecon1: Recon-all
-autorecon1 -subjid FoM04_KA
Does anyone have any suggestions as to what I could do? It
would be
greatly appreciated. I've attached a screenshot to illustrate.
Also, we used a
4.7T Varian scanner with 0.375/0.375/1mm voxels. I believe we
used a
gradient echo multislice sequence. In addition, all subjects'
data have been
obtained so there is no chance of changing sequences?
Best wishes,
Dan
__**_
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
__**_
Freesurfer mailing list
[Freesurfer] What is CSF label is aseg.stats
Dear all, I read the others posts about CSF but I didn't find the information that I need. I would like to calculate total CSF and in the aseg.stats file there are : Lateral-Ventricle, Inf-Lat-Vent, 3rd Ventricle, 4th Ventricle, 5th Ventricle but what is CSF ? Because I read that freesurfer can't measure sulcus CSF so I don't understand what is the meaning of CSF alone. Thank you for your answer ! Sophie ___ 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] What is CSF label is aseg.stats
Hi Sophie I think it's little bits of CSF sulcal and otherwise that for some reason the CMA included in their labeling. I don't think it will contribute much, but should be included. cheers Bruce On Tue, 22 Jan 2013, Sophie Maingault wrote: Dear all, I read the others posts about CSF but I didn?t find the information that I need. I would like to calculate total CSF and in the aseg.stats file there are : Lateral-Ventricle, Inf-Lat-Vent, 3rd Ventricle, 4th Ventricle, 5th Ventricle but what is CSF ? Because I read that freesurfer can?t measure sulcus CSF so I don?t understand what is the meaning of ?CSF? alone. Thank you for your answer ! Sophie ___ 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] tracula bedpostx failure
Hello Experts, I am running bedpost x through fsl on the dmri directory (as advised in a previous post). I receive the fsl error message: “child process exited abnormally”. The command line error states: switching from /8000_tracula/8000_tracula_out/8005_DTI/dmri to /8000_tracula/8000_tracula_out/8005_DTI bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 /Applications/fsl/bin/bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 subjectdir is /8000_tracula/8000_tracula_out/8005_DTI/dmri /8000_tracula/8000_tracula_out/8005_DTI/dmri/data not found All the output files of the trac-all -prep stage are there, but could I have made a mistake on my configuration file? I have attached it. Thank you very much for your help, Cheers, Cat dmrirc_single_subject Description: Binary data ___ 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] long_mris_slopes / mris_calc problem
I was able to solve my problem in my earlier email included below. I downloaded a new verison of mris_calc made it executable with chmod +x FILE and then replaced it in the bin folder. I included this response in case anyone else runs into the same problem and does a search. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to prepare the data using this command: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage It seems to run fine at first but after a minute or so it hits this command and crashes: mris_calc -o /Applications/freesurfer/subjects/SPIN073/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-SPIN073_lh_thickness_igG3e9/beta1.mgh div ./tmp-SPIN073_lh_thickness_igG3e9/beta0.mgh It prints: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? And then returns to my command prompt. I searched online and found someone last year asked the same question here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-September/020311.html However the response links to an updated version of mris_calc but when I click the link it says I do not have permission the access. Thanks for any help in advance. -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] question about persession versus perrun motion correction
Hi Dough, This might be a very basic question: I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line: *mkanalysis-sess \* * -analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* * -native -mcextreg -stc siemens -fwhm 0 \* * -event-related -paradigm para_cat.par -nconditions 5 \* * -spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* * * * * * And here is what I have in my analysis info analysis Cat_1 mcstem fmc fsd bold runlistfile run_1.txt TR 2 RegDOF 6 RawSpace volume native mask brain RawFWHM 0 RawSTC siemens UseB0DC 0 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 5 parname para_cat.par RefEventDur 3 timewindow 40.00 prestim 0 TER 0.05 spmhrf 0 stimulusdelay -1. Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 nuisreg mcextreg 3 I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1. M * ___ 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] question about persession versus perrun motion correction
Hi Maryam, when you say that they are practically identical, I assume that there are at least some small differences indicating that something was different? And what are you comparing exactly? Eg, single subject or group? In principle, they should be pretty close to each other, it depends entirely on how much the subject moved between runs and how much smoothing you apply. If you have a well-behaved population, then there might not be much of a difference. If you reduce the smoothing to 0, then you might start to see more of an effect. doug On 01/22/2013 02:44 PM, Maryam Vaziri Pashkam wrote: Hi Dough, This might be a very basic question: I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line: *mkanalysis-sess \* *-analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* *-native -mcextreg -stc siemens -fwhm 0 \* *-event-related -paradigm para_cat.par -nconditions 5 \* *-spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* * * * * * And here is what I have in my analysis info analysis Cat_1 mcstem fmc fsd bold runlistfile run_1.txt TR 2 RegDOF 6 RawSpace volume native mask brain RawFWHM 0 RawSTC siemens UseB0DC 0 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 5 parname para_cat.par RefEventDur 3 timewindow 40.00 prestim 0 TER 0.05 spmhrf 0 stimulusdelay -1. Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 nuisreg mcextreg 3 I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1. M * -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] question about persession versus perrun motion correction
I am comparing the final beta.nii.gz by importing it to matlab and this is on individual subjects. The subjects have not moved much (less than 3 mm). But the number of voxels that have different values in betta.nii.gz are a handful which does not seem right since the fmc.nii.gz and fmcpr.nii.gz are much more differet. Also the X.mat file should contain the motion correction values since I have asked the analysis to use motion as an external regressor. But the two X.mat files in the analysis folder in the bold directory are very very similar (not identical but the difference seems to be in the 0.01 range that might be due to some rounding errors) One thing that puzzles me is the -funcstem in the analysis.info which is set to fmc by default. Does this force the analysis to use fmc.nii.gz az the input to the analysis? Should I make it to use fmcpr for the perrun analysis to get different results? M On Tue, Jan 22, 2013 at 2:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Maryam, when you say that they are practically identical, I assume that there are at least some small differences indicating that something was different? And what are you comparing exactly? Eg, single subject or group? In principle, they should be pretty close to each other, it depends entirely on how much the subject moved between runs and how much smoothing you apply. If you have a well-behaved population, then there might not be much of a difference. If you reduce the smoothing to 0, then you might start to see more of an effect. doug On 01/22/2013 02:44 PM, Maryam Vaziri Pashkam wrote: Hi Dough, This might be a very basic question: I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line: *mkanalysis-sess \* *-analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* *-native -mcextreg -stc siemens -fwhm 0 \* *-event-related -paradigm para_cat.par -nconditions 5 \* *-spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* * * * * * And here is what I have in my analysis info analysis Cat_1 mcstem fmc fsd bold runlistfile run_1.txt TR 2 RegDOF 6 RawSpace volume native mask brain RawFWHM 0 RawSTC siemens UseB0DC 0 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 5 parname para_cat.par RefEventDur 3 timewindow 40.00 prestim 0 TER 0.05 spmhrf 0 stimulusdelay -1. Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 nuisreg mcextreg 3 I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1. M * -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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/**compliancelinehttp://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] Results Vary
also there is an issue in v5.1 where the second run of recon-all on a given platform will produce different results from the first (but subsequent runs should produce identical results). this issue has been fixed in the upcoming v5.2 release. nick On Tue, 2013-01-22 at 10:18 -0500, Douglas N Greve wrote: Hi Chikku, while we try to resolve these differences, you are not guaranteed to get identical results when you use different platforms. This is an issue with using different computes and applies to all software, not just FS.It is caused by the use of different math libraries and different binary operations. The difference you show is only 0.3% which should not be enough to cause false results. doug On 01/22/2013 08:13 AM, Varghese Chikku wrote: Dear FS team, I processed two set of MRI data for a single patient,Thats BL scan and TP1.I ran both scans on a Mcbook Pro and a PC with Virtual machine installed. Though I was expecting the same segstats,the results vary from Macpro to VM.For eg , for BL in Mac SubCortGrayVol is 178038 but for the same images in VM the results are 177432.Does it happened to any one beforeWhats the reson its happening and how can I remedy,validate the results. Much appreciate your advice,... In Thanks Chikku. ___ 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.
Re: [Freesurfer] question about persession versus perrun motion correction
Oh, right, I remember now (at least mostly). I fixed that for version 5.2. Maryam, it may be that the code is not actually using the persession data like it should. doug On 01/22/2013 03:19 PM, r...@nmr.mgh.harvard.edu wrote: Hi Doug, There at least used to be a bug in the way perrun/persession was handled. We exchanged emails about that about a years ago (see especially Tapsya's emails). If I recall correctly we were never able to make this work without rigging the file extensions etc (FS-FAST always defaulted to one stream and/or one file extension regardless of which option was used). Not sure if this is still a problem, but could be related to Maryam's email. Cheers, Tommi Hi Maryam, when you say that they are practically identical, I assume that there are at least some small differences indicating that something was different? And what are you comparing exactly? Eg, single subject or group? In principle, they should be pretty close to each other, it depends entirely on how much the subject moved between runs and how much smoothing you apply. If you have a well-behaved population, then there might not be much of a difference. If you reduce the smoothing to 0, then you might start to see more of an effect. doug On 01/22/2013 02:44 PM, Maryam Vaziri Pashkam wrote: Hi Dough, This might be a very basic question: I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line: *mkanalysis-sess \* *-analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* *-native -mcextreg -stc siemens -fwhm 0 \* *-event-related -paradigm para_cat.par -nconditions 5 \* *-spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* * * * * * And here is what I have in my analysis info analysis Cat_1 mcstem fmc fsd bold runlistfile run_1.txt TR 2 RegDOF 6 RawSpace volume native mask brain RawFWHM 0 RawSTC siemens UseB0DC 0 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 5 parname para_cat.par RefEventDur 3 timewindow 40.00 prestim 0 TER 0.05 spmhrf 0 stimulusdelay -1. Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 nuisreg mcextreg 3 I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1. M * -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] freesurfer@nmr.mgh.harvard.edu
Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward). Thanks a lot in advance, Nicola ___ 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] Downsampling/decimating overlays (not surfaces)
Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward). Thanks a lot in advance, Nicola PS apologies for the repost - my subject line was incorrect the first time around. ___ 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] question about persession versus perrun motion correction
also I am have not done any smoothing so that means that I should expect some differences between the beta values across the two analysis. M On Tue, Jan 22, 2013 at 3:00 PM, Maryam Vaziri Pashkam mvazir...@gmail.comwrote: I am comparing the final beta.nii.gz by importing it to matlab and this is on individual subjects. The subjects have not moved much (less than 3 mm). But the number of voxels that have different values in betta.nii.gz are a handful which does not seem right since the fmc.nii.gz and fmcpr.nii.gz are much more differet. Also the X.mat file should contain the motion correction values since I have asked the analysis to use motion as an external regressor. But the two X.mat files in the analysis folder in the bold directory are very very similar (not identical but the difference seems to be in the 0.01 range that might be due to some rounding errors) One thing that puzzles me is the -funcstem in the analysis.info which is set to fmc by default. Does this force the analysis to use fmc.nii.gz az the input to the analysis? Should I make it to use fmcpr for the perrun analysis to get different results? M On Tue, Jan 22, 2013 at 2:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Maryam, when you say that they are practically identical, I assume that there are at least some small differences indicating that something was different? And what are you comparing exactly? Eg, single subject or group? In principle, they should be pretty close to each other, it depends entirely on how much the subject moved between runs and how much smoothing you apply. If you have a well-behaved population, then there might not be much of a difference. If you reduce the smoothing to 0, then you might start to see more of an effect. doug On 01/22/2013 02:44 PM, Maryam Vaziri Pashkam wrote: Hi Dough, This might be a very basic question: I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line: *mkanalysis-sess \* *-analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* *-native -mcextreg -stc siemens -fwhm 0 \* *-event-related -paradigm para_cat.par -nconditions 5 \* *-spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* * * * * * And here is what I have in my analysis info analysis Cat_1 mcstem fmc fsd bold runlistfile run_1.txt TR 2 RegDOF 6 RawSpace volume native mask brain RawFWHM 0 RawSTC siemens UseB0DC 0 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 5 parname para_cat.par RefEventDur 3 timewindow 40.00 prestim 0 TER 0.05 spmhrf 0 stimulusdelay -1. Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 nuisreg mcextreg 3 I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1. M * -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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/**compliancelinehttp://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
Re: [Freesurfer] tracula bedpostx failure
Hi Cat - I hope this helps: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25987.html a.y On Tue, 22 Jan 2013, Cat Chong wrote: Hello Experts, I am running bedpost x through fsl on the dmri directory (as advised in a previous post). I receive the fsl error message: “child process exited abnormally”. The command line error states: switching from /8000_tracula/8000_tracula_out/8005_DTI/dmri to /8000_tracula/8000_tracula_out/8005_DTI bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 /Applications/fsl/bin/bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 subjectdir is /8000_tracula/8000_tracula_out/8005_DTI/dmri /8000_tracula/8000_tracula_out/8005_DTI/dmri/data not found All the output files of the trac-all -prep stage are there, but could I have made a mistake on my configuration file? I have attached it. Thank you very much for your help, Cheers, Cat ___ 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] Empty search space
Dear FS experts I run a longitudinal analysis, and all steps (cross, base, long) were run without errors. I used QA tools in order to look at the results and all recons are fine. However, when running glmfit with the --osgm option there is no error message, but there is also no results (sig=0, F=0). In the log I realized that the mask is empty (see below). Found 149955 points in label. Pruning voxels by thr: 0.00 Found 0 voxels in mask Saving mask to Cap_Thickness_LH.glmdir/mask.mgh Reshaping mriglm-mask... search space = 0.00 What are the most plausible reasons for this empty mask? Should I try the pruning option? Thanks in advance Regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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.
