[Freesurfer] denominator of the t-test in fsfast?

freesurfers, i have a question about how t-tests are computed in fsfast. so t = ces/sqrt(cesvar), but how exactly is cesvar calculated? i thought it would be: cesvar = variance_of_residual *c*(X' * X)^-1*c' where X is the stim matrix and c is the contrast vector and ' denotes transpose

Re: [Freesurfer] How to get surface-based AAL template

I faced this problem a while ago. Both MNI to fsaverage, MNI itself and Colin27 didn't work sufficiently for sampling the labels, all had problems with the registration causing holes in the sulci and gyri ending up in the wrong label. (That might be 'good' since AAL is a volumetric atlas; but

[Freesurfer] FS 5.2 asegstats2table is not found or is too small to be a valid stats file error

Dear Experts, I am trying to extract FS 5.2 statistics for a single subject using the following command: asegstats2table --subjects SUBJECTNAME --tablefile teststats.txt I keep getting *the following error: * *The stats file /PATH/SUBJECTNAME/stats/aseg.stats is not found or is too small to

Re: [Freesurfer] denominator of the t-test in fsfast?

Hi Alex, On 3/31/13 7:37 AM, Alex Kell wrote: freesurfers, i have a question about how t-tests are computed in fsfast. so t = ces/sqrt(cesvar), but how exactly is cesvar calculated? i thought it would be: cesvar = variance_of_residual *c*(X' * X)^-1*c' where X is the stim matrix and c

[Freesurfer] tractstats@table output oddity

Subject: [Freesurfer] tractstats@table output oddity I ran tractstats2table to make a table of my dti tract stats for the fmajor_PP tract see the attached script file @tractstats2table and the file list fmajor_file_list.txt it produced the output file fmajor_table.txt (attached) in

Re: [Freesurfer] mri_glmfit-sim doesn't recognize --label flag

Hi Cherry, you need to run mri_glmfit with the --label flag. Then run mri_glmfit-sim without a label flag. mri_glmfit-sim will see that you used a label and incorporate it. doug On 3/30/13 7:02 PM, Yizhou Ma wrote: Dear freesurfer experts, I'm doing small volume correction for multiple

Re: [Freesurfer] FS 5.2 asegstats2table is not found or is too small to be a valid stats file error

does that file exist? On 3/31/13 12:11 PM, Salil Soman wrote: Dear Experts, I am trying to extract FS 5.2 statistics for a single subject using the following command: asegstats2table --subjects SUBJECTNAME --tablefile teststats.txt I keep getting *the following error: * *The stats file

Re: [Freesurfer] How to get surface-based AAL template

Hi Zhi Liang, Out of curiosity, why not just use the FreeSurfer parcellations, so you don't end up with holes in the sulci/gyri? --Thomas On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk martijnsteenw...@gmail.com wrote: I faced this problem a while ago. Both MNI to fsaverage, MNI itself and