Eachoutput.nii.gz sess1/bold/analysis folder will have a dof.dat file with a number in it. Add up all those numbers, create a files with the sum in it, and pass that file to mrI_gomfit.
On 04/27/2015 06:18 PM, Reza Rajimehr wrote: > 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 > <mailto: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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
