I am having a problem similar to that previously described on the freesurfer 
message boards from May 2011 (Subject: mgh conversion).  Unfortunately, that 
thread ends with Doug asking the person to send him the files in question, so 
there does not appear to be any sort of publicly published solution.  

I was sent two .mgh files with the resulting activation maps from an fMRI 
analysis (both left and right hemispheres) and told that the maps were in 
fsaverage space.  I was not sent any other accompanying files.  I am trying to 
convert them to nii format.

I have tried both:
1. mri_convert filename.mgh filename.nii.gz 

and mri_surf2surf (as was suggested in the previous thread)

2. mri_surf2surf —sval filename.mgh —tval filename.nii —reshape —reshape-factor 
6 —s fsaverage —hemi lh

(I realize that the command options should be preceded by double dashes, but my 
email program is quite insistent about automatically formatting these to long 

In both cases the when checking the output file using mri_info, the dimensions 
are still: 163842 x 1 x 1.

Are there any suggestions as to how best to proceed?  

Thanks in advance,

Suzanne Witt

Freesurfer mailing list

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