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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