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 <greve@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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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.