[Freesurfer] alloc: invalid block

Hi, I am following the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OverlayFeatStatisticalMaps At this command, tksurfer bert lh inflated -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 -fmid 3.3 -fslope 1

Re: [Freesurfer] displaying the result of group analysis in thickness or p-value

Woo-Suk, The results displayed in qdec are the p-values. Currently, display of mean group thickness is not available, but will be available in a future version of qdec (although it should be understood that mean group thickness is outside of the GLM and contrast analysis, so no statistical signif

Re: [Freesurfer] recon-all error @ mris_volmask...

Nick, I don't know if this is important but when I try to send these subjects to seychelles and continue the recon process where it left off the job errors immediately, but if I specify a node (-l nodes=1:P4) the job seems to run. Are the updated VTK libraries currently only available to certain no

Re: [Freesurfer] recon-all error @ mris_volmask...

Cameron and Padraig, This is a problem local to the NMR Center (MGH), where the VTK libraries (of which mris_volmask makes use) were recently updated, and the update contains a bug. I'm working on a local fix now, which should be ready within an hour (locally). The public freesurfer is not affec

Re: [Freesurfer] recon-all error @ mris_volmask...

Hi, Two things: 1) Try running mris_volmask from the command line and see if it runs. You may be missing a library (I recall having a similar error). 2) Running out of memory might be a factor. How much do you have? Padraig Cameron Ellis wrote: Hi, I am receiving this error for every subjec

[Freesurfer] recon-all error @ mris_volmask...

Hi, I am receiving this error for every subject I send through recon-all. I am checking for edits that need to be made but it seems very odd that 30 subjects or so would all error out at the same step. Any suggestions? Cameron Subject 'Ponce_033d2': make all recon-all -s /autofs/space/grouch_004/

Re: [Freesurfer] Aseg.stats file

Thanks. That seemed to work just fine. Jared Bruce Fischl wrote: I think recon-all -subjid -segstats should do itOn Wed, 30 Jan 2008, Jared Conley wrote: FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally

Re: [Freesurfer] Aseg.stats file

Jared, You can do recon-all -segstats for each subject. This uses the aseg.mgz to create the aseg.stats, however, if the new aseg.mgz you generated with the script I sent you is named something other than aseg.mgz, then you will want to change it to aseg.mgz for this to work. Allison On We

[Freesurfer] Aseg.stats file

FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally for a few subjects and we wondered if we could quickly recreate this file without having to run recon-all again. All the other files in the subject directory are

Re: [Freesurfer] Aseg.stats file

I think recon-all -subjid -segstats should do itOn Wed, 30 Jan 2008, Jared Conley wrote: FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally for a few subjects and we wondered if we could quickly recreate this

[Freesurfer] displaying the result of group analysis in thickness or p-value

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #66; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear FreeSurfer experts.I have finished the Free