[Freesurfer] Yeo_JNeurophysiol11_FreeSurfer.zip

Hello, I'm trying to download ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_FreeSurfer.zip (as linked from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011), however, the file doesn't seem to be available, or the server is not responsive. Is there another locatio

[Freesurfer] Mapping annotation files from one subject to another

Hello, I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so? I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error. First I ran mris_ca_train lh lh.sphere.reg fsaverage/l

Re: [Freesurfer] Mapping annotation files from one subject to another

like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work. Thanks, Peter On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote: > Hi Peter, > mri_surf2surf is what you want to use for this. > -Louis &

Re: [Freesurfer] Mapping annotation files from one subject to another

is for. What was your command line? Did you > check the help? > > On Tue, 18 Jun 2013, Peter Savadjiev > wrote: > >> Hi Louis, >> >> When I try mri_surf2surf, I get the error >> ERROR: could not determine type of Yeo2011_7Networks_N1000.annot >> >> C

Re: [Freesurfer] Mapping annotation files from one subject to another

Oh, I see what my error was: I need to use --sval-annot instead of --srcsurfval. Thanks! Peter On 06/18/2013 02:51 PM, Bruce Fischl wrote: > this is what mri_surf2surf is for. What was your command line? Did you > check the help? > > On Tue, 18 Jun 2013, Peter Savadjiev > wrote

[Freesurfer] mri_surf2vol

Hi, I am trying to convert the "curv" surfaces to a volume, using the mri_surf2vol command in the following manner: cd subjects/subjid mri_surf2vol --surf curv --hemi lh --template ./mri/orig.mgz --outvol /tmp/curv.mgz --surfval ./surf/lh.curv --fillribbon --volregidentity subjid I get the fo

Re: [Freesurfer] mri_surf2vol

: > subjid should be the name of your subject (not literally "subjid") > > Peter Savadjiev wrote: >> Hi, >> >> I am trying to convert the "curv" surfaces to a volume, using the >> mri_surf2vol command in the following manner: >> >> cd subje

Re: [Freesurfer] mri_surf2vol

las N Greve wrote: > Oh, don't use --surf curv. The curv is not a surface (which has vertex > XYZ and neighborhood relationships). Leave that option off (to get > white) or specify a real surface. > doug > > Peter Savadjiev wrote: >> Hi Douglas, >> >> Yes, I kn

Re: [Freesurfer] mri_surf2vol

You are right, it turned out there was an issue with $SUBJECTS_DIR and when I fixed it, everything worked fine. Thank you very much for your help! Peter On 09/16/2011 03:22 PM, Douglas N Greve wrote: > Is that subject in your $SUBJECTS_DIR ? > > Peter Savadjiev wrote: >> Hi D

[Freesurfer] question about annot files and principal curvatures

Hi, In order to obtain the vertices of lh.curv that belong to a specific freesurfer cortical ROI, such as 'superiortemporal', or 'superiorfrontal', etc., I use the information in lh.aparc.annot, as described for example in http://surfer.mnr.mgh.harvard.edu/fswiki/AnnotFiles/ . However, now I

Re: [Freesurfer] question about annot files and principal curvatures

rfaces for a given subject in the same > hemisphere. > > cheers > Bruce > On Thu, 19 Jan 2012, Peter Savadjiev wrote: > >> Hi, >> >> In order to obtain the vertices of lh.curv that belong to a specific >> freesurfer cortical ROI, such as 'superi

Re: [Freesurfer] question about annot files and principal curvatures

The reason I'm asking is because the mean of the principal curvatures thus obtained differs from the information stored in lh.curv, and I wasn't sure whether this is due to a different ordering of the vertices. Best, Peter On 01/19/2012 10:51 AM, Peter Savadjiev wrote: > Thanks Br