Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

FreeSurfer Course Tours, France, 26-27/05/2016
by Christophe Destrieux 12 Feb '16

12 Feb '16

Dear FreeSurfers, It is our pleasure to welcome you the FreeSurfer course organized in Tours, Loire Valley, France, 2016 26-27th may. This event is coorganized by the brain and imaging laboratory, INSERM U930-Université François Rabelais of Tours (France) and by the Martinos Center for Biomedical Imaging in Charlestown, MA (USA) which develops and distributes FreeSurfer. <http://freesurfer.net/> This course will be limited to 64 participants. It will focus on surface-based analysis of individual and group morphological data and on tractographic analysis using FreeSurfer tools. This course will be organized in the Ecole Polytechnique de l'Université de Tours For online registration, please visit : http://freesurfer2016.sciencesconf.org/?lang=en See you in Tours next May C Destrieux, F Andersson, L Barantin, S Love, M Sta, C Tauber Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

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R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 11 Feb '16

11 Feb '16

I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz When I open with freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad reoriented, especially I have noted this on subcortical connectivity (MNI2mm). Thanks Stefano ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 11-feb-2016 4.48 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST I may have gotten the exact form of the flag wrong. When it says an option is not known, you should try running the command with --help to see if something similar is there. In this way, you might be able to figure it out for yourself rather than have to wait a day or so for us to respond. doug On 2/10/16 4:20 PM, stdp82(a)virgilio.it wrote: If I use: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon ERROR: Option --fill-ribbon unknown ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 8-feb-2016 20.35 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST Thanks. I have down a right ad left ROI on the surface. Next, I have run: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz mri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.config fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config fcseed-sess -s subj1_FS -cfg LEFT_ROI.config but during fcseed-sess this error occurs: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh Segmentation fault ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 8-feb-2016 4.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM, stdp82(a)virgilio.it wrote: Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer. How can I do it? Should I use mri_label2vol? Thanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 11 Feb '16

11 Feb '16

I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz When I open using freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad reoriented, especially I have noted this on subcortical connectivity (MNI2mm). Stefano ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 11-feb-2016 4.48 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST I may have gotten the exact form of the flag wrong. When it says an option is not known, you should try running the command with --help to see if something similar is there. In this way, you might be able to figure it out for yourself rather than have to wait a day or so for us to respond. doug On 2/10/16 4:20 PM, stdp82(a)virgilio.it wrote: If I use: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon ERROR: Option --fill-ribbon unknown ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 8-feb-2016 20.35 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST Thanks. I have down a right ad left ROI on the surface. Next, I have run: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz mri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.config fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config fcseed-sess -s subj1_FS -cfg LEFT_ROI.config but during fcseed-sess this error occurs: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh Segmentation fault ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 8-feb-2016 4.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM, stdp82(a)virgilio.it wrote: Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer. How can I do it? Should I use mri_label2vol? Thanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Basal Ganglia Segmentation
by Syeda Wajiha Maryam 11 Feb '16

11 Feb '16

Fear Freesurfer Experts, I have a feeling this question has been asked already but I'm still confused about it. Is there a way to extract the basal ganglia structure using freesurfer? Thanks in advance for your help! Regards, Maryam

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FreeSurfer MRI segmentation
by Maheen Siddiqui 11 Feb '16

11 Feb '16

Dear FreeSurfer Users, I have a T1 weighted MRI scan and have run the recon-all command on it. For my steps moving forward I need to have 4 layers of tissue i.e. 4 segmentation files - GM, WM, CSF and extra cerebral tissue. Which of the outputs from recon-all will give me the segmentation? I thought at first that brain.mgz was what I needed but having viewed brain.mgz in Freeview, it is just the skull stripped version of the T1 scan. Is there any document that details all the outputs of recon-all? Many thanks for any advice I can get! Maheen

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comparison between two hemisphere in single subject
by Ashkan Faghiri 11 Feb '16

11 Feb '16

Hello, I want to compare the two hemisphere in one subject (thickness for example). should I use? surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi then what? how can I compare the two hemisphere of one subject? Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology

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Processing of young children using Freesurfer
by Zoellner, Frank 11 Feb '16

11 Feb '16

Hi, I am currently working on a project involving brain morphometry of 2 year old children. We are interested in segmenting the ventricle and I tried to run freesurfer using the standard recon-all -all for a first test. Unfortunately, freesurfer reports an error (see attached log file). I also read about that it is advised to run freesurfer with patient age >5 but maybe someone has an idea how to solve this. As far as I get from the step it crashes at the intensity correction step? Do I need to calculate some sort of template maybe ? Any comments welcome Yours Frank ---------------- PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner(a)MedMa.Uni-Heidelberg.de<mailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

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Re: [Freesurfer] To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 10 Feb '16

10 Feb '16

If I use: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon ERROR: Option --fill-ribbon unknown ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 8-feb-2016 20.35 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST Thanks.I have down a right ad left ROI on the surface.Next, I have run: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gzmri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgzmri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.configfcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config fcseed-sess -s subj1_FS -cfg LEFT_ROI.config but during fcseed-sess this error occurs: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user StefanoUseRobust 0Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gzLoading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gzVoxel Volume is 64.5752 mm^3Generating list of segmentation idsFound 1 segmentationsComputing statistics for each segmentation 0 1 0 0.000MRIalloc(0, 1, 1): bad parmReporting on 0 segmentationsComputing spatial average of each frameWriting to /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mghSegmentation fault ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 8-feb-2016 4.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM, stdp82(a)virgilio.it wrote: Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer. How can I do it? Should I use mri_label2vol? Thanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

difference in 001.mgz found
by Krieger, Donald N. 10 Feb '16

10 Feb '16

These runs were executed on the Open Science Grid. So the data file, the scan, was uploaded to grid worker machine, placed in a transitory directory, and processed. The full pathname of the file is included in 001.mgz. I got it by: zcat mri/orig/001.mgz | strings Here are the input and output file names for 2 of the runs: /var/lib/condor/execute/dir_31034/MRN_1_defaced.mgz /scratch/tmp.FFTGBhmgp8/MRN_1/mri/orig/001.mgz /var/lib/condor/execute/dir_3734674/glide_HRFaAm/execute/dir_3741395/MRN_1_defaced.mgz /scratch/tmp.ghJfB4leGR/MRN_1/mri/orig/001.mgz Best - Don > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer- > bounces(a)nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N. > Sent: Wednesday, February 10, 2016 6:38 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] comparing multiple runs on the same scan > > It looks like they do give the same results. > I have to write something to go through everything systematically which I may > not get to till tomorrow. > Also I am checking to see whether there was some difference in how 001.mgz > was created. > The source image file on which we are running freesurfer is a defaced.mgz . > It's possible that it was sitting in a different directory for the different runs > since the runs were executed by a work flow management system (Pegasus) on > the Open Science Grid. > > Don > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer- > bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [greve(a)nmr.mgh.harvard.edu] > Sent: Wednesday, February 10, 2016 6:13 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] comparing multiple runs on the same scan > > That probably means that there is something in the header that is different. It > should print a report to the terminal. Do they not give the same results? > > On 02/10/2016 04:36 PM, Krieger, Donald N. wrote: > > mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are > different. > > In fact, their sizes are slightly different. > > > > > > > >> -----Original Message----- > >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer- > >> bounces(a)nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > >> Sent: Wednesday, February 10, 2016 3:45 PM > >> To: Freesurfer support list > >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan > >> > >> Hi Don > >> > >> are you saying the 001.mgz is different when created from the same > >> dicom data? Can you run mri_diff on it to see what the difference is? > >> > >> cheers > >> Bruce > >> On Wed, 10 > >> Feb 2016, Krieger, Donald N. wrote: > >> > >>> We would like to confirm that we are getting identical results from > >>> multiple freesurfer runs on the same data set. > >>> > >>> To do so we are comparing identically named files using md5sum and > >>> would very much appreciate your thoughts on our results. For > >>> multiple files, we concatenate them and pipe the output into md5sum. > >>> Below is a table showing what we’ve found so far. I take hope from > >>> the positive matches we get from all of the .annot files and from > >>> the fact that 001.mgz does not match. This latter suggests that > >>> there is a date or something embedded in some of the files from > >>> separate runs which > >> defeats the match. > >>> > >>> > >>> Please let us know what you know about this and thanks. > >>> > >>> > >>> > >>> file(s) > >>> > >>> md5sum result > >>> > >>> label/*.annot > >>> > >>> match > >>> > >>> label/*.label > >>> > >>> match > >>> > >>> mri/wmparc.mgz > >>> > >>> mismatch > >>> > >>> surf/qsphere.nofix > >>> > >>> surf/rh.sphere > >>> > >>> mismatch > >>> > >>> mri/orig/001.mgz > >>> > >>> mismatch > >>> > >>> mri/transforms/talairach.m3z > >>> > >>> match > >>> > >>> mri/transforms/talairach.m3z.inv.x.mgz > >>> > >>> mri/transforms/talairach.m3z.inv.y.mgz > >>> > >>> mri/transforms/talairach.m3z.inv.z.mgz > >>> > >>> mismatch > >>> > >>> mismatch > >>> > >>> mismatch > >>> > >>> > >>> > >>> Best - Don > >>> > >>> > >>> > >>> > >>> > >>> Don Krieger, Ph.D. > >>> > >>> Department of Neurological Surgery > >>> > >>> University of Pittsburgh > >>> > >>> > >>> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 2

comparing multiple runs on the same scan
by Krieger, Donald N. 10 Feb '16

10 Feb '16

We would like to confirm that we are getting identical results from multiple freesurfer runs on the same data set. To do so we are comparing identically named files using md5sum and would very much appreciate your thoughts on our results. For multiple files, we concatenate them and pipe the output into md5sum. Below is a table showing what we've found so far. I take hope from the positive matches we get from all of the .annot files and from the fact that 001.mgz does not match. This latter suggests that there is a date or something embedded in some of the files from separate runs which defeats the match. Please let us know what you know about this and thanks. file(s) md5sum result label/*.annot match label/*.label match mri/wmparc.mgz mismatch surf/qsphere.nofix surf/rh.sphere mismatch mri/orig/001.mgz mismatch mri/transforms/talairach.m3z match mri/transforms/talairach.m3z.inv.x.mgz mri/transforms/talairach.m3z.inv.y.mgz mri/transforms/talairach.m3z.inv.z.mgz mismatch mismatch mismatch Best - Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh

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