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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