Re: [Freesurfer] A question as to subcortical volumetric measurement
Dear Doug Thank you so much. Your comment would be of great help to me. Kim 2013/11/7 Douglas N Greve gr...@nmr.mgh.harvard.edu The FS segmentation is a combined segmentation and registration to an atlas space. This is probabilistic in that the atlas is built from 40 subjects and uses intensity, location, and neighborhood priors. I think VBM is using unified segementation which performs intensity normalization, segmentation, and registration simultaneously also using a probabilistic atlas. VBM segments GM/WM/CSF whereas FS segments various GM and ventricular structures as well as WM. VBM is a voxelwise analysis which is registered to an atlas, modulated, and spatially smoothed, all of which will have strong effects on the results. Maybe a VBM expert on the list can chime in with more info. doug On 11/05/2013 08:08 PM, jh kim wrote: Dear Drs. Bruce and Doug Thanks for the valuable comments. Discrepancy between FS and VBM lies in putamen and hippocampus. Would you please briefly comment regarding segmentation method of above structures in FS? I'm just wondering whether segmentation of grey matter in FS is largely different from that of VBM? Sorry for bothering you again with my silly question. Thanks. Kim 2013/11/5 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Kim, the answer is both easy and difficult. The easy answer is that they are completely different methods and will often give inconsistent results. I'm not sure what answer the reviewer will accept, and you might need to post the same question to the VBM and DARTEL crews. In your VBM analysis, I assume that you used modulation (ie, you were looking at volume and not GM density)? VBM performs a voxel by voxel comparison and you probably smoothed by 10mm or so. Either of those could have washed out the effect. Certainly a reasonable response is that the FS analysis is for the entire ROI and and the VBM is voxelwise. Hope that help.s doug On 11/03/2013 11:55 PM, jh kim wrote: Dear Doug and experts I've analyzed structural changes of the subcortical GM by using both VBM (DARTEL in SPM8) and subcortical volumemetric measurement using FreeSurfer 5.1. While there is no significant volumetric difference between the groups in VBM (corrected p0.05), FS results showed that some subcortical GM had significant volume reductions in patients relative to controls (MANCOVA controlling for the effect of ICV, age, gender, followed by Bonferroni correction). One of the referees raised the question regarding this discrepancy between the VBM and FS findings. How can I cope with it? Thank you in advance for your help. Kim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: 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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
[Freesurfer] Literature values of cortical thickness
Dear Freesurfer experts, I need to compare the cortical thickness values, obtained from a data set of 32 healthy subjects, with some reference literature values of cortical thickness. I'd like to check the values of mean and standard deviation for each one of the 32 cortical parcellations automatically generated by Freesurfer. This is to decide if the data set can be used for the following steps of my work or not. On the mailing list, I read an old thread that talks about the existence of a set of literature reference values, obtained by Rauhl Desikan. Would it be possible to access those data? Thank you Emma Biondettu ___ 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] MRISread error
It finally worked! Thank you so much Louis. My SUBJECTS_DIR was pointing to a folder within my TUTORIAL_DATA directory (I thought it was supposed to be like that when I read the instructions), but now they point to the same folder and it works. Thanks again! Anita ___ 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]Cohen'd effect size map
Dear freesurfer experts In qdec I use the DODS degsin to obtain the thickness difference between my two groups with age ,gender as nuisance.Then I want to get the effect size map instead of report the significance level. In freesurfer wiki I found that we can obtain the effect size map via gamma/sqrt(gammavar*Npilot), where Npilot is the number subjects in the pilot study.While I have two groups,one control group with 25 subjects and one patient group with 25 subjects too,I doubt that which number I should use ,the number of patient group subjects 25 or for the whole subjects across groups 50 to repalce the Npilot in the equation? And then I look for previous relevant topic in the freesurfer mail list, found that doug suggested that we can get the effect size just use gamma/rstd, I tried for that but found completely different result between I use the equation of gamma/sqrt(gammavar*Npilot), which equation should I use for I want to get the Cohen'd effect size map? Thank you in advance for your helps! Ji Chen___ 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] Literature values of cortical thickness
Hi Emma this is a bit of a dicey thing to do as the thickness value are senstive to non-biological things like field strength. You can look in our original PNAS thickness paper and we published values for a number of regions and compared them to e.g. Von Economo, but in the end the best you can do is to visually inspect the surfaces for placement accuracy. cheers Bruce On Thu, 7 Nov 2013, Emma Biondetti wrote: Dear Freesurfer experts, I need to compare the cortical thickness values, obtained from a data set of 32 healthy subjects, with some reference literature values of cortical thickness. I'd like to check the values of mean and standard deviation for each one of the 32 cortical parcellations automatically generated by Freesurfer. This is to decide if the data set can be used for the following steps of my work or not. On the mailing list, I read an old thread that talks about the existence of a set of literature reference values, obtained by Rauhl Desikan. Would it be possible to access those data? Thank you Emma Biondettu ___ 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] Problems with autorecon2-cp
Hi Annemarie It's tough to tell from the single slice. Make sure that the control points are in voxels that are entirely white matter. If you put them in the gray it will mess everything up. If you upload the subject we will take a look cheers Bruce On Thu, 7 Nov 2013, Annemarie Brandhofe wrote: Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have been experiencing a problem with the automatic recognition of the control points. After setting the control points and running autorecon2-cp white matter segmentation is faulty in almost every slice. I attached screenshot of two slices. Can you recommend us a procedure to improve the automatic recognition of control points? Below, we provide the details of our setup. Feel free to ask for more information. Thank you very much for your help! Yours sincerely, Annemarie $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-5.3.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39-1-ql-beowulf i686 $ which freesurfer - /apps/prod/i486/freesurfer-5.3.0/bin/freesurfer Used command: recon-all ?autorecon2-cp ?subjid ET39_mdeft. ___ 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] MRISalloc: could not allocate vertices
Hi Freesurfers, Got this error while running some of my subjects: Correcting Topology of defect 1 with euler number -257 (129 loops) computing statistics for defect 1: 33364 vertices location: [ (156,125,84) - average intensity = 92.126 ] -gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 ) -gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 ) -intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ]) -curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 ) -curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 ) MRISalloc(8654176, 520): could not allocate vertices Cannot allocate memory Do anyone know how to fix this? Thanks, -Siddharth ___ 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] mris_fix_topology hangs (?)
Hi, I'm running recon-all on a subject from the human connectome project, and for some reason mris_fix_topology seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem? Best, Martin PS: I'm using FS 5.3 ... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514 CORRECTING DEFECT 0 (vertices=65102, convex hull=346) ___ 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] ltaReadFile error while running recon-all -long
My mistake, this was user error involving renaming directories. jon On Nov 6, 2013, at 4:25 PM, Jonathan Holt whats...@umich.edu wrote: FS experts, I’m having a bit of an issue with a single subject. Recon-all -long errors out after it tells me it cannot open the subjid_to_template.lta file. I’m very confused, because the file it’s looking for exists in the exact location it’s looking for but the recon-all.log suggests that there is no such file or directory. It proceeds to map control points and runs into a segmentation fault, after which it exits with errors. Any help would be appreciated. ___ 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] MRISalloc: could not allocate vertices
Hi Siddharth 33364 is a pretty big defect and typically means something is pretty badly wrong with your data. This can mean that the hemis are connected, or attached to the skull or cerebellum. Take a look at the ?h.orig.nofix and see if you can figure out what is going wrong. You'll need to diagnose it before you can correct it (either by adding control points, or editing the wm.mgz typically) cheers Bruce On Thu, 7 Nov 2013, Ray, Siddharth wrote: Hi Freesurfers, Got this error while running some of my subjects: Correcting Topology of defect 1 with euler number -257 (129 loops) computing statistics for defect 1: 33364 vertices location: [ (156,125,84) - average intensity = 92.126 ] -gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 ) -gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 ) -intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ]) -curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 ) -curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 ) MRISalloc(8654176, 520): could not allocate vertices Cannot allocate memory Do anyone know how to fix this? Thanks, -Siddharth ___ 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] mris_fix_topology hangs (?)
Hi Martin see my response to a similar question just a minute or two ago. This is the same issue (a defect that is too big) cheers Bruce On Thu, 7 Nov 2013, Martin Luessi wrote: Hi, I'm running recon-all on a subject from the human connectome project, and for some reason mris_fix_topology seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem? Best, Martin PS: I'm using FS 5.3 ... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514 CORRECTING DEFECT 0 (vertices=65102, convex hull=346) ___ 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] mris_fix_topology hangs (?)
Hi Bruce, Thanks, this makes sense. I somehow assumed 1 defect wouldn't be bad but failed to notice how large the defect is. I was using the -washu_mprage option as it is for the HCP data and the gm looked quite dark to me. I will try to run FS without that option. Best, Martin On 11/07/13 11:17, Bruce Fischl wrote: Hi Martin see my response to a similar question just a minute or two ago. This is the same issue (a defect that is too big) cheers Bruce On Thu, 7 Nov 2013, Martin Luessi wrote: Hi, I'm running recon-all on a subject from the human connectome project, and for some reason mris_fix_topology seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem? Best, Martin PS: I'm using FS 5.3 ... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514 CORRECTING DEFECT 0 (vertices=65102, convex hull=346) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Luessi, Ph.D. Research Fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 Fax: +1 617 726-7422 ___ 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] mris_fix_topology hangs (?)
We are not using the -washu_mprage option in the HCP pipelines. My understanding is that flag dates way back to when WashU was running a non-standard MPRAGE. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 11/7/13 10:28 AM, Martin Luessi mlue...@nmr.mgh.harvard.edu wrote: Hi Bruce, Thanks, this makes sense. I somehow assumed 1 defect wouldn't be bad but failed to notice how large the defect is. I was using the -washu_mprage option as it is for the HCP data and the gm looked quite dark to me. I will try to run FS without that option. Best, Martin On 11/07/13 11:17, Bruce Fischl wrote: Hi Martin see my response to a similar question just a minute or two ago. This is the same issue (a defect that is too big) cheers Bruce On Thu, 7 Nov 2013, Martin Luessi wrote: Hi, I'm running recon-all on a subject from the human connectome project, and for some reason mris_fix_topology seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem? Best, Martin PS: I'm using FS 5.3 ... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere. nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514 CORRECTING DEFECT 0 (vertices=65102, convex hull=346) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Luessi, Ph.D. Research Fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 Fax: +1 617 726-7422 ___ 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_fix_topology hangs (?)
yes, it is quite old and applies to a set of mprage parameters that result in *very* dark gray matter (the gray is actually closer to CSF than white matter in that sequence). Thanks for pointing this out Mike Bruce On Thu, 7 Nov 2013, Harms, Michael wrote: We are not using the -washu_mprage option in the HCP pipelines. My understanding is that flag dates way back to when WashU was running a non-standard MPRAGE. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 11/7/13 10:28 AM, Martin Luessi mlue...@nmr.mgh.harvard.edu wrote: Hi Bruce, Thanks, this makes sense. I somehow assumed 1 defect wouldn't be bad but failed to notice how large the defect is. I was using the -washu_mprage option as it is for the HCP data and the gm looked quite dark to me. I will try to run FS without that option. Best, Martin On 11/07/13 11:17, Bruce Fischl wrote: Hi Martin see my response to a similar question just a minute or two ago. This is the same issue (a defect that is too big) cheers Bruce On Thu, 7 Nov 2013, Martin Luessi wrote: Hi, I'm running recon-all on a subject from the human connectome project, and for some reason mris_fix_topology seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem? Best, Martin PS: I'm using FS 5.3 ... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere. nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514 CORRECTING DEFECT 0 (vertices=65102, convex hull=346) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Luessi, Ph.D. Research Fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 Fax: +1 617 726-7422 ___ 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fMRI-data mri_convert, missing header
The vision is a very old scanner. Does it actually output DICOM? 15 years ago it only output IMA files. If so, then try mri_convert -it siemens file.ima file.mgh On 11/05/2013 06:54 AM, Philipp Heimbeck wrote: Hello! I'm encountering a problem with converting fMRI-Data from dicom- to NIfTI-files (single file). The problem only occurs with data aquired on Siemens Vision, data from Siemens Trio work just fine. The Siemens ASCII header is missing (files have not been anonymized) and every dicom-file has its own series number. This is true for all functional data (10 subjects, one run each). Other programs can't convert these dicom-files either (dcm2nii, NIfTI-1 converter for BVQX). Do you know if there is a possible solution for this problem? In more detail, when running mri_convert, the following happens: ... Getting Series No Scanning Directory INFO: Found 218 files in ../run INFO: Scanning for Series Number 67 INFO: found 1 files in series INFO: loading series header info. INFO: sorting. RunNo = 66 WARNING: file ../MR.9500.260 does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (512 512 1), nframes = 1, ismosaic=0 PE Dir COL COL FileName../MR.9500.260 Identification NumarisVerVB33D ScannerModel MAGNETOM VISION PatientName deleted, shows correctly Date and time StudyDate deleted, shows correctly StudyTime 150948.046000 SeriesTime153015.877000 AcqTime 153606.293000 Acquisition parameters PulseSeq ep_fid Protocol unknown PhEncDir COL EchoNo1 FlipAngle 90 EchoTime 60 InversionTime -1 RepetitionTime60 PhEncFOV 0 ReadoutFOV0 Image information RunNo 66 SeriesNo 67 ImageNo 260 NImageRows512 NImageCols512 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 96. 80.1658 98.1990 VolRes 0.3750 0.3750 3. VolDim512 5121 Vc -1. 0. -0. Vr -0. -0.9848 -0.1736 Vs-nan -nan -nan VolCenter -nan -nan -nan TransferSyntaxUID unknown INFO: no Siemens slice order reversal detected (good!). TR=60.00, TE=60.00, TI=-1.00, flip angle=90.00 i_ras = (-1, 0, -0) j_ras = (-0, -0.984808, -0.173648) k_ras = (-nan, -nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -0.375 -0.000 -nan -nan; 0.000 -0.369 -nan -nan; -0.000 -0.065 -nan -nan; 0.000 0.000 0.000 1.000; If there's any help, I'm glad to hear it. And if the answer is no, the data is gone forever, this would be a helpful response, too. Philipp ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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] [freesurfer]Cohen'd effect size map
I think the gamma/rstd what you want. doug On 11/07/2013 08:14 AM, 陈骥 wrote: Dear freesurfer experts In qdec I use the DODS degsin to obtain the thickness difference between my two groups with age ,gender as nuisance.Then I want to get the effect size map instead of report the significance level. In freesurfer wiki I found that we can obtain the effect size map via gamma/sqrt(gammavar*Npilot), where Npilot is the number subjects in the pilot study.While I have two groups,one control group with 25 subjects and one patient group with 25 subjects too,I doubt that which number I should use ,the number of patient group subjects 25 or for the whole subjects across groups 50 to repalce the Npilot in the equation? And then I look for previous relevant topic in the freesurfer mail list, found that doug suggested that we can get the effect size just use gamma/rstd, I tried for that but found completely different result between I use the equation of gamma/sqrt(gammavar*Npilot), which equation should I use for I want to get the Cohen'd effect size map? Thank you in advance for your helps! Ji Chen ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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] Segmentation question
FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi ___ 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 question
Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi ___ 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] Is there anyway to define multiple processing cores for FreeSurfer to speed up its commands?
Hello, I'm using FreeSurfer on a 6-core Mac Pro machine. It takes quite a bit for commands like recon-all to complete, while I've noticed that my CPU and memory resources are mostly idle. I just wanted to know if there's anyway to define multiple cores for FreeSurfer (something like matlabpool in matlab parallel computing toolbox). Thank you, Emad Emad Ahmadi, MD Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.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] Segmentation question
Hi Rashmi, Several of the morphometry stats were changed between 5.1 and 5.3. I don't remember the specifics, but Doug or someone else on the list may know. Alternatively, you could use the mri_segstats from 5.3 to calculate the morphometry stats for your 5.1 data. -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: I am using version V5.1.0 is it different for that or the information is the same irrespective of the version I use. Rashmi On 11/7/13 1:57 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi 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 question
Here is the recon-all table for 5.1, see the segstats step. You can also search for that flag in the recon-all script and see what input/flags are passed to mri_segstats. https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1 On Thu, 7 Nov 2013, Rashmi Singh wrote: Can you tell me what is the input file that free surfer used to calculate STV. I am not sure the webpage below gives that information. Thanks, Rashmi On 11/7/13 1:57 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi 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 question
Can you tell me what is the input file that free surfer used to calculate STV. I am not sure the webpage below gives that information. Thanks, Rashmi On 11/7/13 1:57 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi 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] Is there anyway to define multiple processing cores for FreeSurfer to speed up its commands?
Hi Emad, If there is something like that I would be quite interested in a way to do so as well as I'm working on a scalable Freesurfer cloud setup, but all I know so far is, that you can parallelize parts of the freesurfer pipeline to two parallel tasks. I think it's autorecon2, probably even autorecon3 which has an optional parameter for the hemisphere to use, and if you call it without it calculates them in a row, first the left hemisphere and then the right (or vice versa). If you instead call it twice in separate processes once with left and once with right hemisphere, you parallelize this step accordingly. If there's anything more I have no idea - but I would be interested in it as well (provided that it's not on the cost of numerical stability or something like that) regards Peter Am 07.11.2013 21:42, schrieb Emad Ahmadi: Hello, I'm using FreeSurfer on a 6-core Mac Pro machine. It takes quite a bit for commands like recon-all to complete, while I've noticed that my CPU and memory resources are mostly idle. I just wanted to know if there's anyway to define multiple cores for FreeSurfer (something like matlabpool in matlab parallel computing toolbox). Thank you, Emad Emad Ahmadi, MD Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.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
[Freesurfer] algorithm developer position open
Hi! All, We have an algorithm developer position open at Synarc. If you are interested, please send me your resume. Position Description: The algorithm developer engineer works with our scientific groups to come up innovative image processing and data mining/pattern recognition algorithms to maintain scientific lead in all TA areas Responsibilities: Work with Scientists and TA lead on surveying literature /algorithms and existing commercial implementation for specific tasks. Prototype and validating algorithms on large dataset by using in house cluster or Amazon EC2. Prototype related UI elements and addressing integration on Synarc internal proprietary platform. Work with Scientists and TA lead on journal/conference publications and intellectual properties related document. Qualifications: Education: PhD in biomedical engineering, physics, applied math or computer science Experience: Must be expert in ITK and Matlab Familiar with HPC like condor or SGE is a must have Experience with EC2 will be a plus Experience with VTK or QT will be a plus. Experience with Python/Java/SQL will be a plus Skills: Good written and verbal communication skills. Good problem solving, technical troubleshooting, organizational, interpersonal and team skills. Gennan Chen Engineering Manager, Synarc This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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] error using selxavg3-sess for resting state connectivity
Hi there We are performing a connectivity analysis using a seed mask we have drawn from a label on the average surface in tksurfer. We put the label into subject surface space using mri_label2label then made the label into a volume using mri_label2vol. We then extracted the seed timecourse using fcseed-config and fcseed-sess. We then have a text file containing the seed region timeseries in the fMRI data folder. We then ran mkanalysis-sess with the -notask flag and after the -taskreg flag we input the seed region timeseries text file. mkanalysis-sess -a connectivity -surface fsaverage lh -notask -taskreg Sess01/rest/001/connect_FEF2FEF.txt 1 -nuisreg Sess01/rest/001/ica_reg.txt -1 -fsd rest -TR 2.5 When we run selxavg3-sess after this we get an error after it starts matlab: ERROR: cannot find volume matching /data/project2/pMelb0036/om_2013/freesurfer/project/Sess01/rest/001/Sess01/rest/001/connect_FEF2FEF.txt ERROR: loading nonpar reg /data/project2/pMelb0036/om_2013/freesurfer/project/Sess01/rest/001/Sess01/rest/001/connect_FEF2FEF.txt -- ERROR: fast_selxavg3() failed\n I'm not sure why it can't find the file as it's definitely there in the directory containing fmcpr.nii can anyone help? many thanks Scott ___ 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.
