Thanks Doug! Could you clarify a bit more on how to "add up the dofs in each run"?
You can mri_concat the cesvar files. For the dof, just add up the dofs in each run. On Monday, April 27, 2015, Reza Rajimehr <rajim...@gmail.com> wrote: > 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 > <javascript:_e(%7B%7D,'cvml','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> 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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