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Ok. i figured it out. The problem was just that you can not specify the file type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem.
Now I run in a new issue:
gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'
Wed Jan 8 17:04:12 CET 2020
setenv SUBJECTS_DIR /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects cd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects /usr/local/freesurfer/bin/gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo
$Id: mri_gtmseg.c,v 1.10 2016/08/02 21:07:24 greve Exp $ cwd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects cmdline mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild subject 1122_test USF 2 OutputUSF 2 apasfile BN_apas+head.mgz wmannotfile NULL ctxannotfile BN_Atlas.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 0 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 mri_gtmseg supposed to be reproducible but seed not set Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/1122_test/mri/BN_apas+head.mgz Loading surfaces t = 2.1510 Loading annotations t = 4.8510 Not segmenting WM reading colortable from annotation file... colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt) reading colortable from annotation file... colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt) Relabeling any unlateralized hypointenities as lateralized hypointenities MRIrelabelHypoHemi(): looping over volume nthreads = 1 Relabeling CC as WM Relabeling any hypointensities as WM MRIunsegmentWM(): looping over volume nthreads = 1 Upsampling segmentation USF = 2 t = 7.3520 MRIhiresSeg(): filling unknowns with 257 Beginning cortical segmentation using BN_Atlas.annot t = 41.3800 MRIannot2CorticalSeg(): looping over volume nthreads = 1 MRIannot2CorticalSeg(): found 2347 unknown, filled with 257 Not subsegmenting WM Found 279 segs in the final list MRIgtmSeg() done, t = 224.1820 Computing colortable ERROR: cannot find match for subcortical segid 227 ERROR: mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt --no-subseg-wm --no-keep-cc --no-keep-hypo gtmseg exited with errors
Before I run gtmseg I used xcerebralseg --s 1122_test --m aparc+BN_Atlas_subcotex.mgz --atlas '/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_subcortex.gca' --o BN_apas+head.mgz
Any ideas on that?
Best, Boris
Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu>:
Are you sure you have permission to view that file?
On 1/6/20 5:01 PM, Boris Rauchmann wrote:
External Email - Use CautionI’m sure just double checked it. I don’t know what’s wrong here.
Von meinem iPhone gesendet
Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu>:
This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder?
On 1/3/20 3:07 PM, Boris Rauchmann wrote:
External Email - Use CautionThank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here?
Best, Boris
MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
Reading lh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
Loading lh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
Reading rh pial surface /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
Loading rh annotations from /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial ERROR: cannot find aseg MacBook-Pro:mri boris$
Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>: OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again? On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
External Email - Use CautionMy-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Users/boris/Desktop/mydir/1122/surf/lh.white Reading lh pial surface /Users/boris/Desktop/mydir/1122/surf/lh.pial Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Reading rh white surface /Users/boris/Desktop/mydir/1122/surf/rh.white Reading rh pial surface /Users/boris/Desktop/mydir/1122/surf/rh.pial Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial ERROR: cannot find aseg I get the same result using aseg.mgz Thanks, Boris > Am 12.12.2019 um 17:37 schrieb Bruce Fischl > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>: > Hi Boris > can you send us the full command line and screen output of the > commands that are failing? > cheers > Bruce > On Thu, 12 Dec 2019, Boris Rauchmann wrote: >> External Email - Use Caution >> Thanks. unfortunately I get an error message when I use the --aseg >> flag for BN_Atlas_subcotex.mgz but >> even, if I'm using the original aseg.mgz I get: ERROR: cannot find >> aseg >> .../fs_all_subjects/xyz/mri/aseg.mgz >> The file BN_Atlas_subcotex.mgz was created using: >> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz >> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z >> $SUBJECTS_DIR/BN_Atlas_subcortex.gca >> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz >> Best, >> Boris >> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: >> What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but >> with your >> subcortical ROIs added? If so, you can try merging it with >> the aparc, eg, >> mri_aparc2aseg --s subject --volmask --aseg >> BN_Atlas_subcotex.mgz --o >> aparc+BN_Atlas_subcotex.mgz >> Then use aparc+BN_Atlas_subcotex.mgz as input to >> xcerebralseg, and then >> run gtmseg as you have done below. >> Let me know if that works >> doug >> On 12/2/19 1:18 PM, Boris Rauchmann wrote: >> > >> > External Email - Use Caution >> > >> > In this example tried it with only the subcortical >> segmentations from >> > my atlas. Please find the logfile attached. It gives me >> back: "tissue >> > type is not set" but I set it to 2 in the LUT.txt >> > >> > In principle look the following commands right to you? >> > >> > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m >> > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca >> > >> > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab >> > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz >> > >> > Ideally I would have a gtmseg with both, the subcortical >> and the >> > cortical structures, but only the subcortical would also be >> fine as >> > long as I can get mri_gtmpvc running on it. >> > >> > Thanks, >> > Boris >> > >> > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. >> > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> wrote: >> > >> > Can you send the log file for each of the gtmseg runs? >> > >> > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> >> >> External Email - Use Caution >> >> >> >> Thank you! I have a gca for subcortical and two gcs >> (lh/rh) for >> >> cortical structures. >> >> I created an annot (rh/lh) and a mgz using
mris_ca_label
>> >> and mri_ca_label for parcellation/segmentation stats. >> >> >> >> For the PET analysis I have the following problem: >> >> >> >> If I use this command: gtmseg --s test --o test.mgz
--ctab
>> >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz >> >> --ctx-annot BN_Atlas.annot --ctab >> '/xyz/BN_Atlas_246_LUT.txt' >> >> >> >> It gives me the right regions for subcortical >> structures but it >> >> looks like it uses the standard FS parcellation with >> my labels >> >> for the cortical parcellations (only 93 cortical >> regions instead >> >> of 210). >> >> >> >> If I use gtmseg --s 0059test --o
onlyhead.gtmseg_test.mgz
>> >> --ctx-annot BN_Atlas.annot --ctab >> '/xyz/BN_Atlas_246_LUT.txt' >> >> --no-xcerseg I get all my 210 cortical parcellations >> but the >> >> standard FS subcortical segmentations. >> >> >> >> How can I use both in one gtmseg so that I can >> proceed with it >> >> doing my PET analysis in PETSurfer? It is not totally >> clear for >> >> me what to merge using xcerebralseg. >> >> >> >> Thanks a lot! >> >> >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas
N.,Ph.D.
>> >> <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >> wrote: >> >> >> >> It gets the subcortical from apas+head.mgz which >> gets created >> >> along the >> >> way by xcerebralseg. You can create your own with >> >> xcerebralseg by >> >> specifying your volume as the mergevol. I think >> this will >> >> work, but I'm >> >> not sure. I'm assuming you've used the GCA to >> create your own >> >> subcortical seg for the given subject >> >> >> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >> >> > >> >> > External Email - Use Caution >> >> > >> >> > I just realized that the above mentioned command >> (gtmseg >> >> --s XYZ --o >> >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >> >> > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> >> --no-xcerseg) >> >> > gives me only the cortical segmentation. Is >> there any way >> >> to also >> >> > include the subcortical segmentation based on my >> individual >> >> atlas? I >> >> > also have an Atlas_subcortex.gca file available. >> >> > >> >> > Best, >> >> > Boris >> >> > >> >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas >> N.,Ph.D. >> >> > <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >> >> mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu>> wrote: >> >> > >> >> > There is no cut off for the minimum size. As >> it gets >> >> smaller, the PVC >> >> > noise amplification will become bigger (it >> also depends >> >> on the >> >> > shape as >> >> > well). >> >> > >> >> > I think the --no-xcerseg is the right way to >> go now >> >> > >> >> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >> >> > > >> >> > > External Email - Use Caution >> >> > > >> >> > > Thank you for your prompt answer - the
command
>> >> worked. This is the >> >> > > atlas mentioned: >> >> http://atlas.brainnetome.org/brainnetome.html >> >> http://atlas.brainnetome.org/brainnetome.html >> >> > > What is approximately the smallest >> possible segment >> >> when using PVC? >> >> > > Also, does the exclusion of extracerebral >> structures >> >> harm? I >> >> > used that >> >> > > flag because it complained: >> >> > > >> >> > > gtmseg --s XYZ --o BN.gtmseg.mgz
--ctx-annot
>> >> BN_Atlas.annot --ctab >> >> > > >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> >> > > ERROR: >> /media/subjects/XYZ/mri/apas+head.mgz exists. >> >> This is ok >> >> > > but you must indicate whether to use what >> is there >> >> (--no-xcerseg) >> >> > > or create a new one and overwrite what is >> there >> >> (--xcerseg) >> >> > > or specify your own headseg (--head) >> >> > > >> >> > > and did not want to override my
apas+head.mgz
>> >> > > >> >> > > Thanks, >> >> > > Boris >> >> > > >> >> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, >> Douglas N.,Ph.D. >> >> > > <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> >> mailto:DGREVE@mgh.harvard.edu >> >> mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu> >> >> > mailto:DGREVE@mgh.harvard.edu > >> mailto:DGREVE@mgh.harvard.edu >> >> mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu>>> >> >> > wrote: >> >> > > >> >> > > I don't know what the Brainnetome is, >> but it >> >> looks like you have >> >> > > it in >> >> > > annotation form. I think that command
should
>> >> work. Why are >> >> > you using >> >> > > --no-xcerseg? This will cause it to not >> include >> >> extracerebral >> >> > > structures. Also note that you cannot use >> >> arbitrarily small >> >> > segments >> >> > > when doing PVC. >> >> > > >> >> > > On 8/13/19 10:26 AM, Boris Rauchmann >> wrote: >> >> > > > >> >> > > > External Email - Use Caution >> >> > > > >> >> > > > Dear all, >> >> > > > >> >> > > > my intention is to use the >> Brainnetome Atlas >> >> > > parcellation/segmentation >> >> > > > in PETSurfer to obtain PVC corrected >> SUVRs for >> >> the atlas >> >> > ROIs. I >> >> > > used: >> >> > > > >> >> > > > gtmseg --s XYZ --o BN.gtmseg.mgz >> --ctx-annot >> >> > BN_Atlas.annot --ctab >> >> > > > >> >> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >> >> > --no-xcerseg >> >> > > > >> >> > > > Is this the right approach to obtain >> a high >> >> resolution >> >> > > segmentation to >> >> > > > run PVC methods? >> >> > > > >> >> > > > Thanks, >> >> > > > Boris >> >> > > > >> >> > > > >> _______________________________________________ >> >> > > > Freesurfer mailing list >> >> > > > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > > <mailto:
Freesurfer@nmr.mgh.harvard.edu
>> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > > > >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > > >> >> > > >> >> > > >> _______________________________________________ >> >> > > Freesurfer mailing list >> >> > > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > > >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > > >> >> > > >> >> > > >> _______________________________________________ >> >> > > Freesurfer mailing list >> >> > > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > > >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu > >> mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edu>
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