External Email - Use Caution
Thanks a lot!
On 16 July 2018 at 18:47, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote:
> You can also use mri_concat to compute the mean, eg,
> mri_concat file1.mgh file2.mgh ... fileN.mgh --mean --o average.mgh
>
> On 07/13/2018 11:17 AM, Bruce Fischl wrote:
> > Hi Elisa
> >
> > if you only use --s fsaverage, then mri_surf2surf assumes you are
> > mapping within subject. If you want to map from one subject to another
> > you need to use --srcsubject sub01 --trgsubject fsaverage
> >
> > And yes, if you get that working I think fscalc should do the trick
> > (or it would be easy to do in matlab).
> >
> > cheers
> > Bruce
> > On Fri, 13 Jul 2018, Elisa Castaldi wrote:
> >
> >>
> >> External Email - Use Caution
> >>
> >> Dear experts,
> >>
> >> I would like to show the across-subject overlap of voxels by creating
> >> a map with color coding
> >> indicating the number of subjects activating corresponding voxels.
> >> For each subject I have run the first level model in spss and saved
> >> the 1000 most activated voxels
> >> for a given contrast as an roi (binary file).
> >> Now with freesurfer I am trying to :
> >> 1) display the saved roi on the subject's surface (which has been
> >> obtained with recon all) - this
> >> step worked
> >> 2) align each subject's surface to fsaverage - this step gave me the
> >> problem
> >> 3) add all subjects together and create the map showing how many
> >> subjects activated each location
> >>
> >> To do so I have done the following:
> >>
> >> 1) this first step worked fine and I could display the roi on my
> >> subject's surface
> >> mri_vol2surf --mov ${DATA_DIR}/sub01/vois/1000vox_IPS.nii \
> >> --reg ${DATA_DIR}/sub01/fmri/register.dat \
> >> --hemi rh \
> >> --o ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh \
> >> --projfrac ${thisprojfrac}
> >>
> >> 2) this step crashed
> >> mri_surf2surf --hemi rh --s fsaverage --fwhm 3 --cortex \
> >> --sval ${DATA_DIR}/sub01/probmap/testIPS.rh.mgh --tval
> >> ${DATA_DIR}/sub01/probmap/testIPSfs.mgh
> >>
> >> The error is:
> >> Loading source data
> >> ERROR: dimension inconsistency in source data
> >> Number of surface vertices = 163842
> >> Number of value vertices = 133030
> >>
> >> Do you have any idea why?
> >>
> >> 3)Then I was planning to use fscalc and add all subjects together, is
> >> this correct?
> >>
> >> If there is another/easier way to do the same thing, please let me know
> >> Thanks in advance for your help,
> >> Best
> >> Elisa
> >>
> >>
> >
> >
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