Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

Re: [Freesurfer] Dimension Mismatch Error
by Michelle Umali 04 Oct '11

04 Oct '11

Hi Doug and Freesurfers, No matter what I try I am still getting the Dimension mismatch error when running fieldsign-sess. I even ran recon-all -s sj12 -make all. I don't think it's a problem with the directories (below). The subjectname file is correct, and when I run field-sign-sess it sees the anatomical directory. What else do you recommend? Thanks. Michelle On Mon, Oct 3, 2011 at 4:36 PM, Michelle Umali <mumali01(a)gmail.com> wrote: > Hi Doug, > I keep my retinotopy (sj) and anatomical (ld) data separate. I named the > retinotopy directory sj12 with the subjectname file says ld12, which is the > anatomical directory for the same subject. > > -Michelle > > > On Mon, Oct 3, 2011 at 4:31 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > > wrote: > >> Can you check that the subjectname file is correct? In some cases, it >> looks like it is using subject sj12, in others it looks like it is using >> subject ld12. >> doug >> >> Michelle Umali wrote: >> >>> Hi Doug, >>> >>> I re-ran from preproc-sess using the -force flag, and I still get the >>> same dimension mismatch error. >>> >>> I'm attaching the terminal output starting from pre-proc-sess. >>> >>> What's the next step? >>> >>> Thanks. >>> Michelle >>> >>> On Mon, Oct 3, 2011 at 3:23 PM, Douglas N Greve < >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >>> wrote: >>> >>> You can an asynchrony between your fmri data and the anatomical: >>> Anatomical: num vertices: 146530 >>> fMRI: 158944 vertices >>> >>> re-run the fMRI starting from preproc-sess. You will need to make >>> sure that preproc-sess actually re-runs at least the >>> sample-to-surface. By default, it just looks to see if things are >>> up-to-date (but does not check the anatomical). So, you can run it >>> with -force. This will cause it to re-run everything. Or you can >>> delete the surface files in the bold directories and re-run >>> without -force. >>> >>> doug >>> >>> >>> >>> Michelle Umali wrote: >>> >>> Hi Doug, >>> >>> I've attached the mri_info output on the eccen and polar >>> images as well as the mris_info on the lh.sphere surface >>> >>> Thanks. >>> Michelle >>> >>> On Mon, Oct 3, 2011 at 2:38 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> > >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >>> wrote: >>> >>> Can you send me the result of running mri_info on >>> eccen/real.nii >>> eccen/imag.nii >>> polar/real.nii >>> polar/imag.nii >>> in the >>> /usr/local/freesurfer/**subjects/retinotopy/sj12/bold/* >>> *rtopy.self.lh >>> directory? >>> >>> And the result of >>> mris_info >>> /usr/local/freesurfer/**subjects/retinotopy/sj12/surf/** >>> lh.sphere >>> >>> doug >>> >>> >>> >>> >>> >>> Michelle Umali wrote: >>> >>> Hi Doug, >>> I've attached the output from running fieldsign-sess. >>> >>> Thanks for all your help. >>> Michelle >>> >>> On Mon, Oct 3, 2011 at 12:59 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> >>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>>> >>> wrote: >>> >>> Michelle, before you do that, can you run the >>> offending program >>> with -debug and send me the (copious) terminal >>> output? Your >>> anat >>> should not have to be re-run. >>> >>> doug >>> >>> Michelle Umali wrote: >>> >>> Hi Bruce, >>> Will this undo my wm and pial edits? >>> >>> Thanks. >>> Michelle >>> >>> On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl >>> <fischl(a)nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> >>> > >>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl(a)nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> >>> >> >>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl(a)nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> >>> > >>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl(a)nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> >>> >>> >>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl(a)nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> >>> > >>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl(a)nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> >>> >> >>> >>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl(a)nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> >>> > >>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl(a)nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>>>>>> >>> wrote: >>> >>> try running >>> >>> >>> recon-all -s subject -make all >>> >>> and leave the -dontrun off. It should bring >>> everything up >>> to date >>> >>> Bruce >>> >>> >>> >>> On Sat, 1 Oct 2011, Michelle Umali wrote: >>> >>> Dear Freesurfers, >>> I'm still getting a MRISripZeros() and >>> MRIScopyMRI Surf/src >>> mismatch error >>> when running fieldsign-sess. You >>> suggested that >>> this >>> problem >>> was due to the >>> surfaces being out of synch. When I ran >>> recon-all -s >>> subject >>> -make all >>> -dontrun, I saw that several steps had >>> not run. >>> The data >>> looked alright and >>> the number of vertices matched when I ran >>> -vno-check. >>> >>> The mismatch error is still occurring, and I >>> don't know >>> how to >>> proceed. >>> >>> Please suggest steps that I should take. >>> >>> Thanks. >>> Michelle >>> >>> >>> >>> >>> >>> 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<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 >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> >> >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> >>> >>> >>> https://mail.nmr.mgh.harvard.** >>> edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> >>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>> >>> >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> <tel:617-724-2358 <tel:617-724-2358>> >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 >>> <tel:617-724-2358>>> Fax: 617-726-7422 <tel:617-726-7422> >>> <tel:617-726-7422 <tel:617-726-7422>> >>> <tel:617-726-7422 <tel:617-726-7422> >>> <tel:617-726-7422 <tel:617-726-7422>>> >>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>> FileDrop: >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> <http://www.nmr.mgh.harvard.** >>> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> <http://www.nmr.mgh.harvard.** >>> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> >>> >>> >>> ------------------------------** >>> ------------------------------**------------ >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> >> >>> https://mail.nmr.mgh.harvard.** >>> edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 >>> <tel:617-726-7422> >>> <tel:617-726-7422 <tel:617-726-7422>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >>> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>> >>> >>> ------------------------------**------------------------------** >>> ------------ >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> >>> >>> ------------------------------**------------------------------** >>> ------------ >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >

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tkmedit window size
by Torsten Ruest 04 Oct '11

04 Oct '11

Hi there, I was wondering whether there is better option to resize the tkmedit window: when I drag it bigger, it appears that the same change in aspect ratio is applied to the image I am working on. When using the zoom option (x2), the image I am working on doesn't fit completely into the window anymore, while x1 is too small. Ideally I'd like to drag the window bigger while leaving the image untouched, followed by zooming into to make the image bigger. Is this possible? Thanks very much in advance, Torsten

3 3

(no subject)
by Lugar, Heather 04 Oct '11

04 Oct '11

Can you please tell me if the cerebellum is included in Freesurfer 5.1's total subcortical gray and/or total gray matter volumes? Also, what exactly is included in the total subcortical gray (everything that's produced in the aseg volumes)? Thanks so much, Heather

2 1

Re: [Freesurfer] undo pial edits only
by Torsten Ruest 04 Oct '11

04 Oct '11

to correct the pial surface for incorrect assignment of head tissue, I edit the brainmask.mgz. Hope that's correct... Thanks, Torsten On Tue, 2011-10-04 at 09:07 -0400, Bruce Fischl wrote: > and which volume are you editing? > On Tue, 4 Oct 2011, Torsten Ruest wrote: > > > Hi Bruce, > > > > thanks for your quick reply. No I am editing using the following > > command: > > > > tkmedit PARTICIPANT_FOLDER wm.mgz rh.white -aux brainmask.mgz > > -aux-surface lh.white > > > > Thanks, > > > > Torsten > > > > On Mon, 2011-10-03 at 11:22 -0400, Bruce Fischl wrote: > >> what pial edits to you want to undo specifically? Was it just edits to the > >> brain.finalsurfs.mgz volume? > >> > >> > >> On Mon, 3 Oct 2011, Torsten Ruest wrote: > >> > >>> Hi there, > >>> > >>> I think there is an option to remove all edits that have been > >>> incorporated using recon2 -clean. > >>> > >>> Is there a chance that I can selectively undo all incorporated pial > >>> edits (ie that have been incorporated by running "recon-all -subject > >>> TEST -autorecon2 > TEST-2.log")? > >>> > >>> Thanks very much in advance, > >>> > >>> Torsten > >>> > >>> > >>> > >>> _______________________________________________ > >>> 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. > >> > > > > > >

2 2

FreeSurfer Compiling error
by Jordi Delgado 04 Oct '11

04 Oct '11

Hi FreeSurfers, I'm trying to compile freesurfer with --enable-fermi-gpu and cuda 4. The process stopped with this error message: make[3]: Entering directory `/home/neuro/dev/mri_em_register' /usr/local/cuda/bin/nvcc -o em_register_cuda.o -c em_register_cuda.cu -arch sm_20 --ptxas-options=-v -g -I../include -I../include/dicom -I/home/neuro/mni/current/include em_register_cuda.cu(259): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(262): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(265): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(269): error: calling a host function("TransformGenerator::TransformGenerator") from a __device__/__global__ function("TransformLogps") is not allowed 4 errors detected in the compilation of "/tmp/tmpxft_00007558_00000000-4_em_register_cuda.cpp1.ii". make[3]: *** [em_register_cuda.o] Error 2 make[3]: Leaving directory `/home/neuro/dev/mri_em_register' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/neuro/dev/mri_em_register' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/neuro/dev' make: *** [all] Error 2 I don't know what is going wrong... Any idea? Thank you in advance! -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

2 1

undo pial edits only
by Torsten Ruest 04 Oct '11

04 Oct '11

Hi there, I think there is an option to remove all edits that have been incorporated using recon2 -clean. Is there a chance that I can selectively undo all incorporated pial edits (ie that have been incorporated by running "recon-all -subject TEST -autorecon2 > TEST-2.log")? Thanks very much in advance, Torsten

2 3

Automatic correct of mislabeling around ctx- lateral orbital?
by Knut J Bjuland 04 Oct '11

04 Oct '11

Hi I have processed several subjects using recon-all. However there is problem with non-brain matter being labels as cortex around the eye ball. Are there any automatically methods to correct mislabeling of eye socket as cortex? I am having problem with mislabeling in ctx-lh-lateral orbital and ctx-rh-lateralorbital. Can I issue add any options to the recon-all? Cheers Knut J

2 1

Re: [Freesurfer] Tool for filling
by Ed Gronenschild 04 Oct '11

04 Oct '11

Hi Bruce, I've grabbed the dev version freesurfer-Darwin-leopard-i686-dev.tar.gz (date 2 Oct 2011, 13:10) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ and tried mri_morphology <input vol> fill_holes 26 <output vol> but got the message that the operation "fill_holes" is not supported. Ed

3 3

convert aparc+aseg.mgz to mni305
by Timothy Vickery 03 Oct '11

03 Oct '11

Hi, I'd like to convert a subject's aparc+aseg.mgz to mni305 (2mm) space. So, I ran the following commands (FS 5.1): (from subject's mri directory) mri_vol2vol --mov orig.mgz --tal --s $SUBNAME --o orig.mni2mm.mgz mri_label2vol --seg aparc+aseg.mgz --o aparc+aseg.mni2mm.nii.gz --reg orig.mni2mm.mgz.reg --temp orig.mni2mm.mgz The volume orig.mni2mm.mgz looks totally fine, but the aparc+aseg.mni2mm.mgz is way off -- it is shifted anterior and superior relative to the orig volume. I double-checked orig.mgz and aparc+aseg.mgz, they are totally fine and line up. I also tried this: mri_label2vol --seg aparc+aseg.mgz --o aparc+aseg.mni2mm.nii.gz --regheader orig.mgz --temp orig.mni2mm.mgz This also did not work. Can anyone point out my error? Thanks in advance, Tim

1 0

reg-feat2anat: major failure
by Michelle Umali 03 Oct '11

03 Oct '11

Hi Freesurfers, I've run reg-feat2anat to register my FSL FEAT data to the freesurfer anatomical data. And for most subjects the registration needs a little manual editing (which sometimes includes stretching). But for a few subjects, registration is terrible, e.g. coronal is switched with horizontal or orig surfaces are completely off the FEAT brain. So I looked into my original FEAT directory and FSL's registration between example_func to standard looked fine, but example_func to highres failed. Is there a way to use Freesurfer to register example_func to high res for use in a FEAT analysis so that later reg-feat2anat works? Thanks. Michelle

1 0

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Freesurfer October 2011