Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Viewing nifti file in freeview
by Worker, Amanda 04 Feb '16

04 Feb '16

Hi All, I was hoping someone could help with an issue that I'm having that I'm sure has a simple explanation. I have a proton density map in nifti format that I am trying to convert to mgz using mri_convert. However, when I load the original nifti file into freeview, I get a blank screen and the same when I try to load the converted .mgz - but I have no issue with loading this file into fslview. Other nifti and .mgz files are also loading fine into freeview. Has anyone seen this problem before? Thanks, Amanda

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Re: [Freesurfer] TRACULA Longitudinal can't find subject folder
by Anastasia Yendiki 04 Feb '16

04 Feb '16

Hi Deniz - It seems that it finds the folders of the 2 time points, but not the folder of the longitudinal base template. This is the template that longitudinal recon-all creates in its 2nd processing step. In your case, it would be /data_august/Deniz/DTI_long/subjects/med_AhJa94 Does this exist? a.y On Thu, 4 Feb 2016, Gürsel, Deniz wrote: > Dear Tracula Experts, > > I'm having trouble with longitudinal analysis using tracula. Just to try out, I am > using one subject with 2 time points. I defined the parameters in dmrirc file as: > > set subjlist = (med_AhJa94_1 med_AhJa94_2) > set baselist =(med_AhJa94 med_AhJa94) > > My subject folder which contains the longitudinal templates of reconstruction is > located as "/data_august/Deniz/DTI_long/subjects/med_AhJa94_1.long.med_AhJa94" > "/data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94" > > Tracula can't seem to find this subject folder, although I am providing the correct > parameters for it. I get the error message when I ran trac-all -prep -c > dmrirc.long : > ERROR: cannot find /data_august/Deniz/DTI_long/subjects/med_AhJa94 > > I attached the trac-all.log and dmrirc files for your reference. > Thank you very much. > > > Best regards, > > >

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Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)
by will brown 04 Feb '16

04 Feb '16

Message: 3 Date: Tue, 2 Feb 2016 14:17:02 -0500 From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <E8AA9D81-BB67-446A-BDD8-2000A5AAC28B(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" Hi Will There was no attachment Bruce > On Feb 2, 2016, at 3:27 AM, will brown <willbrown1987(a)gmail.com> wrote: > > Hi Bruce, > > I've attached a shot of the misalignment as seen in freeview. > > Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. > - Ignored: > Thanks, > > Will > > > On Tue, Jan 26, 2016 at 6:00 AM, < freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > > Message: 1 > Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mritotal failed - help with manual > registration > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1601241858240.29174(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Will > > can you take the same images with freeview and send them along? Also: > tell us a bit about your images. What format did they start in? Were they > dicoms? > > Bruce > > On Mon, 25 Jan 2016, will brown wrote: > > > Hi all, > > After attempting recon-all I received the error "mritotal failed, see > > transforms/talairach.log" etc which I understand may have something to do > > with bad output from registration. I've checked orig.mgz which does look out > > of line - the orientation is off so that it appears the subject has their > > head tilted off to one side (see Image1.jpg). > > > > I have tried to fix this manually with the help of this tutorial: > > > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > > > Hovever, the "movable" blurry image that I'm trying to line up with my > > subjects image does not match the coronal, sagittal or horizontal views, > > e.g. when I click "coronal" my subject is displayed correctly but the > > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > > > Am I missing something obvious? (and am I even on the right track given this > > error?) > > > > Thanks in advance for any help. > > > > Cheers, > > Will - Done. 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. ---------- Forwarded message ---------- From: will brown <willbrown1987(a)gmail.com> To: freesurfer-request(a)nmr.mgh.harvard.edu Cc: Date: Thu, 4 Feb 2016 17:07:23 +1300 Subject: Re: mritotal failed - help with manual registration (Bruce Fischl) (Bruce Fischl) Sorry - attached now Message: 3 Date: Tue, 2 Feb 2016 14:17:02 -0500 From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <E8AA9D81-BB67-446A-BDD8-2000A5AAC28B(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" Hi Will There was no attachment Bruce > On Feb 2, 2016, at 3:27 AM, will brown <willbrown1987(a)gmail.com> wrote: > > Hi Bruce, > > I've attached a shot of the misalignment as seen in freeview. > > Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. > > Thanks, > > Will > > > On Tue, Jan 26, 2016 at 6:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > > > Message: 1 > Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mritotal failed - help with manual > registration > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1601241858240.29174(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Will > > can you take the same images with freeview and send them along? Also: > tell us a bit about your images. What format did they start in? Were they > dicoms? > > Bruce > > On Mon, 25 Jan 2016, will brown wrote: > > > Hi all, > > After attempting recon-all I received the error "mritotal failed, see > > transforms/talairach.log" etc which I understand may have something to do > > with bad output from registration. I've checked orig.mgz which does look out > > of line - the orientation is off so that it appears the subject has their > > head tilted off to one side (see Image1.jpg). > > > > I have tried to fix this manually with the help of this tutorial: > > > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > > > Hovever, the "movable" blurry image that I'm trying to line up with my > > subjects image does not match the coronal, sagittal or horizontal views, > > e.g. when I click "coronal" my subject is displayed correctly but the > > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > > > Am I missing something obvious? (and am I even on the right track given this > > error?) > > > > Thanks in advance for any help. > > > > Cheers, > > Will

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Unpacking error
by Ji Won Bang 03 Feb '16

03 Feb '16

Freesurfer team, Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and v5.3.0. The command line is: unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK And I get the error message: $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $ /home/jbang/Projects/replay/log -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ /home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg /home/jbang/Projects/replay/log// Wed Feb 3 18:12:41 EST 2016 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2016/02/03-23:12:41-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: jbang Machine: cpu166.cabiatl.com Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 cpu166.cabiatl.com Linux cpu166.cabiatl.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux Wed Feb 3 18:12:41 EST 2016 Log File is /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log INFO: Logfile is /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile INFO: status file is /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status Scanning directory Wed Feb 3 18:12:41 EST 2016 mri_parse_sdcmdir --sortbyrun --d /home/jbang/Projects/replay/epi//replay01/DICOM/day1 --o /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile --status /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Wed Feb 3 18:17:33 EST 2016 ------------------------------------------ 2 localizer ok 512 512 3 1 00002_loc02.dcm 3 fMRI_physio_1_decoder ok 74 74 33 150 00001_dec01.dcm 5 fMRI_physio_2_decoder ok 74 74 33 150 00001_dec02.dcm 7 fMRI_physio_3_decoder ok 74 74 33 150 00001_dec03.dcm 9 fMRI_physio_4_decoder ok 74 74 33 150 00001_dec04.dcm 11 fMRI_physio_5_decoder ok 74 74 33 150 00001_dec05.dcm 13 fMRI_physio_6_decoder ok 74 74 33 150 00001_dec06.dcm 15 fMRI_physio_7_decoder ok 74 74 33 150 00001_dec07.dcm 17 fMRI_physio_8_decoder ok 74 74 33 150 00001_dec08.dcm 19 fMRI_physio_9_decoder ok 74 74 33 150 00001_dec09.dcm 21 fMRI_physio_10_decoder ok 74 74 33 150 00001_dec10.dcm 23 fMRI_physio_1_retinotopy ok 74 74 33 120 00001_retino01.dcm 25 fMRI_physio_2_retinotopy ok 74 74 32 120 00001_retino02.dcm 27 fMRI_physio_3_retinotopy ok 74 74 32 120 00001_retino03.dcm 29 fMRI_physio_4_retinotopy ok 74 74 32 120 00001_retino04.dcm 31 fMRI_physio_5_retinotopy ok 74 74 32 120 00001_retino05.dcm 35 T1_MEMPRAGE ok 256 256 176 4 00001_T1_MEMPRAGE_35.dcm 36 T1_MEMPRAGE ok 256 256 176 1 00001_RMS.dcm error reading "file4": illegal operation on a directory while executing "gets $FileId line" (procedure "ReadSeqCfg" line 11) invoked from within "ReadSeqCfg $seqcfgfile" invoked from within "if { [info exists seqcfgfile] } { set SeqCfgList [ReadSeqCfg $seqcfgfile]; }" (file "/home/jbang/freesurfer//bin/unpacksdcmdir.tcl" line 1048) This same error message appeared on both v4.5.0 and v5.3.0. Do you have any clue to fix it? Thank you for your help. Best, Ji Won

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Regarding: T2w and HcV analysis
by Dr Sampada Sinha 03 Feb '16

03 Feb '16

Dear freesurefr experts, Hope this mail finds you all doing well. I want to calculate hippocampal subfield volume using T2w mages. Is the recon-all command same as we do for the T1images (recon-all -i input to T1.nii.gz -s 001 -all)? I was not able to understand the recon-all command for the T2w images. if you can please explain it to me: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all what is -i here (which input volume)? Since, -T2 is the T2 images (dcm or nifti) I am going to feed for processing. Appreciate all you help! Best wishes and regards, Sampada -- Sampada Sinha

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Question about mri convert
by Edward Su 03 Feb '16

03 Feb '16

Dear colleagesI am trying to convert my dicom files to .mgz from Freesurfer by using the mri_convert command, but it provides me the following error:edward-virtual-machine:~/freesurfer/subjects/Artists/Controls/C1> mri_convert /home/edward/freesurfer/subjects/Artists/Controls/C1/mprage grappa2x_i0001.dcm mri/orig/001.mgz mri_convert /home/edward/freesurfer/subjects/Artists/Controls/C1/mprage grappa2x_i0001.dcm mri/orig/001.mgz mri_convert: extra argument ("mri/orig/001.mgz") type mri_convert -u for usageCould anybody help me with this problem? Thanks in advance -Edward

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FreeSurfer 6.0 hippocampal subfields error
by Rosanna Olsen 03 Feb '16

03 Feb '16

Dear Eugenio, I am writing because I am getting a mkdir error when I try to run the FreeSurfer 6.0 hippocampal subfields segmentation. I tried moving my installation of freesurfer to a local directory where I have write permission and I also made sure I had write permission in my subject's directory. Do you have any idea what might be causing the error? Thanks in advance! Command and error pasted below: recon-all -s 1001 -sd . -hippocampal-subfields-T1 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 INFO: SUBJECTS_DIR is /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 Actual FREESURFER_HOME /opt/freesurfer6 -rw-rw-r-- 1 rolsen buchsbaum_lab 549732 Feb 3 09:35 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/recon-all.log Linux gateway.neuroinfo.rri 2.6.32-279.9.1.el6.x86_64 #1 SMP Tue Sep 25 21:43:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Feb 3 09:35:59 EST 2016 /opt/freesurfer6/bin/segmentSF_T1.sh /opt/freesurfer6/MCRv80 /opt/freesurfer6 1001 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 left See log file: /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv80/runtime/glnxa64:/opt/freesurfer6/MCRv80/bin/glnxa64:/opt/freesurfer6/MCRv80/sys/os/glnxa64:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/opt/lib.exported Warning: application is running on a locale different from the original platform locale. Error using mkdir Permission denied Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Feb 3 09:36:07 EST 2016 /opt/freesurfer6/bin/segmentSF_T1.sh /opt/freesurfer6/MCRv80 /opt/freesurfer6 1001 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 right See log file: /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv80/runtime/glnxa64:/opt/freesurfer6/MCRv80/bin/glnxa64:/opt/freesurfer6/MCRv80/sys/os/glnxa64:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/opt/lib.exported Warning: application is running on a locale different from the original platform locale. Error using mkdir Permission denied Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #------------------------------------------ Started at Wed Feb 3 09:35:56 EST 2016 Ended at Wed Feb 3 09:36:14 EST 2016 #@#%# recon-all-run-time-hours 0.005 recon-all -s 1001 finished without error at Wed Feb 3 09:36:15 EST 2016 done -- Rosanna Olsen, Ph.D. Scientist, Rotman Research Institute, Baycrest rolsen(a)research.baycrest.org http://research.baycrest.org/rolsen

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Re: [Freesurfer] Freesurfer Digest, Vol 143, Issue 54
by Shady El Damaty 02 Feb '16

02 Feb '16

Thank you ZK! On Thu, Jan 28, 2016 at 4:32 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > On 01/28/2016 01:11 PM, Shady El Damaty wrote: > > Hi, > > > > I was curious to know what the tentative release date for FreeSurfer 6 > is. I?m currently running FreeSurfer on multiple machines with El > Capitan installed and I?m wondering whether it?s worth installing the beta > distribution or rather uninstalling SIP on each of these many machines. > > > > The release date for FreeSurfer 6 has been hard to nail down but we are > in the final stages. I hesitate to give a solid date but I would say a > month is a fair estimate. > > > > Also is there any documentation on any specific bugs to watch out for > with El Capitan and FreeSurfer 5.3? I?ve been running some functions and > haven?t found any errors yet. > > > > I would only expect you to encounter errors if you were calling scripts > which call freesurfer binaries (e.g. recon-all). If your just calling > the binaries themselves then those should run successfully. > > > > > PS - how does FreeSurfer 6 plan to get around SIP? > > We plan on getting around it using two methods. 1) creating wrapper > scripts for some binaries. 2) Adding a source file in existing scripts > to recreate the library path that were stripped by SIP. >

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Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)
by will brown 02 Feb '16

02 Feb '16

Hi Bruce, I've attached a shot of the misalignment as seen in freeview. Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. Thanks, Will On Tue, Jan 26, 2016 at 6:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu > wrote: Send Freesurfer mailing list submissions to freesurfer(a)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-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)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. Re: mritotal failed - help with manual registration (Bruce Fischl) 2. recon -all errors (Jasmin Alves) 3. Re: Processing .mnc files (Ankita Chatterjee) 4. Re: Processing .mnc files (Bruce Fischl) 5. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) 6. hippocampal subfields - multispectral segmentation with FLAIR (Luigi Antelmi) 7. Re: hippocampal subfields - multispectral segmentation with FLAIR (Eugenio Iglesias) 8. Re: recon -all errors (Bruce Fischl) 9. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) 10. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) 11. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) 12. FDR map: hide very little cluster (stdp82(a)virgilio.it) 13. [All] position available immediately (Bruce Fischl) 14. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Douglas Greve) 15. Re: FDR map: hide very little cluster (Douglas Greve) 16. R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) 17. R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) 18. Re: R: Re: FDR map: hide very little cluster (Douglas N Greve) 19. R: R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) 20. Re: R: R: Re: FDR map: hide very little cluster (Douglas N Greve) 21. R: Re: R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) ---------------------------------------------------------------------- Message: 1 Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mritotal failed - help with manual registration To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1601241858240.29174(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Will can you take the same images with freeview and send them along? Also: tell us a bit about your images. What format did they start in? Were they dicoms? Bruce On Mon, 25 Jan 2016, will brown wrote: > Hi all, > After attempting recon-all I received the error "mritotal failed, see > transforms/talairach.log" etc which I understand may have something to do > with bad output from registration. I've checked orig.mgz which does look out > of line - the orientation is off so that it appears the subject has their > head tilted off to one side (see Image1.jpg). > > I have tried to fix this manually with the help of this tutorial: > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > Hovever, the "movable" blurry image that I'm trying to line up with my > subjects image does not match the coronal, sagittal or horizontal views, > e.g. when I click "coronal" my subject is displayed correctly but the > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > Am I missing something obvious? (and am I even on the right track given this > error?) > > Thanks in advance for any help. > > Cheers, > Will

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getting vertex-wise correspondences across subjects
by John Griffiths 02 Feb '16

02 Feb '16

Dear surfers, Could you please help me with the following analysis workflow: I am doing an analysis where I identify patterns on the ?h.orig surfaces. What I want to do now is to resample these patterns over vertices, such that I have vertex-wise correspondence across subjects. I believe this essentially requires the construction of and projection to a group template (although I'm aware this could be done with e.g. fsaverage). Here is where I'm at: cd(freesurfer dir) 1. Read ?h.orig surfaces; compute patterns (...some in-house stuff...) 2. Write patterns out to .mgh file Matlab save_mgh(pat,outfile,eye(4)); Python nibabel.MGHImage(pat[:,numpy.newaxis,numpy.newaxis].astype(np.float32),numpy.eye(4)).to_filename(outfile) 3. Generate group template make_average_subject --out avgsub --sd <fs dir> -subjects subj1 subj2 subj3 .... 4. Register a single example subject to the new group template mris_register -curv subj1/surf/lh.sphere avgsub/lh.reg.template.tif subj1/surf/lh.sphere.reg.avgsub 5. Project the surface patterns identified above on to the new group template, so that the vertex values correspond across subjects, and can be averaged, statistically compared. etc. mri_surf2surf --srcsubject subj1 --srcsurfreg sphere.reg.avg_sub --trgsubject avg_sub --trgsurfreg sphere.reg --hemi lh --sval <pattern mgh file> --tval /tmp/test_avgsub.mgh However this breaks down at mri_surf2surf, and I'm not particularly confident that the earlier parts are exactly right either. Could you please show me what commands I should be using for the aims as described above? Many thanks, John -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics University of Sydney

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