If you have a 3mm MNI152 space, then you should run bbregister to
fsaverage to create a new register.dat file. Alternatively, you can
register it directly to 32k_fs_LR and cut out the middle man (make sure
to use --9 to account for scaling). Please ignore my comment about
fsaverage. In that case it was actually fine.
On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:
Hi Doug,
Thanks for the email. It is in 3mm space, so I guess I should
reslice. Can you please clarify the comment about fsaverage? Does
the --mni152reg flag not apply to that subject? I'm not sure what you
mean about the inclusion indicating ambiguity.
Thanks again,
Rita
On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
The --mni152reg flag is only appropriate if the mov file is in the
2mm mni152 space. The inclusion of fsaverage as the source subject
indicates some ambiguity about this
On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:
Hi,
I'm trying to compare analyses that I've done entirely on the
surface to analyses I've done in the volume. I'm comparing the
analyses by projecting the volume analyses to the surface (HCP's
32k_fs_LR).
The commands I'm using are:
mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi}
--projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii;
mri_surf2surf --srcsubject fsaverage --srcsurfval
${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval
${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL
volumes look identical to the surface analysis, when mapped. (Our
surface analysis is mainly FSL-based, so this makes sense.)
The SPM mapping, however, looks very odd. It isn't just that the
intensity differs, but the localization of high intensity areas
also varies. It seems that everything is shifted a bit superior
and, possibly, posterior to the true location (as seen on the
surface analysis).
I'm wondering if I'm doing anything obviously wrong in my command
usage. The brains were normalized to the MNI ICBM 152 template in
SPM. I *think* it's suitable to use the -mni152reg flag in the
command.
I can attach pictures of the comparison if you'd like.
Thanks in advance,
Rita
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