[Freesurfer] Fwd: Intersection of gray matter and white matter lines - Question

On Dec 24, 2014, at 10:44 PM, Christina Chen wrote: > Hi! > > When looking through the brain scans, I've noticed that the lines outlining white matter intersect with lines outlining the gray matter. Any suggestions on how I fix this problem? > > Thanks, > Christina > ___

Re: [Freesurfer] ATTACHMENT REMOVED--Re: problem with the tracula pre-processing

Hello Anastasia, Everything is fine with the bval and bvec txt files. I've got an error message in tract statistics when I try to run : trac-all -stat -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial [iMac-de-de:freesurfer/subjects/diffusion_tutorial] GdM% trac-all -stat -c $TUTORIAL_DATA/di

Re: [Freesurfer] ATTACHMENT REMOVED--Re: problem with the tracula pre-processing

Giovanni - Glad to hear problems were solved and you got that far! I added the -stat option after the 5.3 release of freesurfer, so you need to download the latest tracula update from here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates Check which build of freesurfer you h

Re: [Freesurfer] ATTACHMENT REMOVED--Re: problem with the tracula pre-processing

Thanks Anastasia for your rapid response. I’ve freesurfer-Darwin-lion-stable-pub-v5.3.0 > Le 10 janv. 2015 à 19:16, Anastasia Yendiki a > écrit : > > $FREESURFER_HOME/build-stamp.txt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

Re: [Freesurfer] ATTACHMENT REMOVED--Re: problem with the tracula pre-processing

Just a last question, it's almost over. I need to select a text file that contains the p-values from my statistical analysis Please, could you give me an example. What statistical analysis ? What file ? in which directory ? Thanks Giovanni > Le 10 janv. 2015 à 19:16, Anastasia Yendiki a > écri

Re: [Freesurfer] ATTACHMENT REMOVED--Re: problem with the tracula pre-processing

The -stat option gives you the FA/MD/RD/AD values along each tract for all subjects in a table. You do whatever statistical analysis on them you want, but you have to do that yourself. On Sat, 10 Jan 2015, de Marco wrote: Just a last question, it's almost over.I need to select a text file t

[Freesurfer] LME Contrasts - Longitudinal Analysis

Dear Freesurfer List, Reading the Wiki for the GLM procedures, I understood that that covariates that are “0” in the contrast matrix are “regressed out” (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V). I would like to know if this is also true for the LME contrasts (http://surfer.nmr.mg

[Freesurfer] selxavg3-sess

Hi list, the selxavg3-sess -s Sess01 -a fc.lpccseed.surf.lh in fcMRI analysis produces this error. rawfunc2surf-sess completed Started at Sun Jan 11 00:50:53 CET 2015 Ended at Sun Jan 11 00:50:54 CET 2015 preproc-sess done -