If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit?
Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr <rajim...@gmail.com> wrote: > Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server > and provide a link so that I can download it? I do not have access to the dev > environment. > > > Now I should run the command with the flag -trgsubject F99, right? > > > My analysis is on the surface, and I only want to concatenate the vertex > values. I have an orig.mgz file in the mri subdirectory of F99, but I hope > isxconcat-sess does not ask for additional volume files. > > > Best, > > Reza > > > > I just fixed this for the dev environment. Try running it from there. > Though I think this is just the start of the problems. > doug > > > > On Monday, April 27, 2015, Reza Rajimehr <rajim...@gmail.com > <javascript:_e(%7B%7D,'cvml','rajim...@gmail.com');>> wrote: > >> Hi, >> >> I am trying to use isxconcat-sess for averaging functional data across >> two monkeys. The data in two monkeys have been analyzed on a common surface >> (F99). When I run this: >> >> isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh >> -all-contrasts -o group2 >> >> I get an error: >> >> ERROR: cannot find >> /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz >> >> Even when I add -trgsubject F99 to the command, I get the same error. >> >> How can I tell isxconcat-sess not to use fsaverage? >> >> I am using Freesurfer v5.3 stable. >> >> Thanks, >> Reza >> >>
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