Hi Bruce,

Thanks for the response.

I actually got this pipeline partly from Thomas a few months back. However, I wasn't sure if anyone had suggestions perhaps for a recon-all based command for going from the MNI152 1mm template-based fit to individual subjects. The recon-all/Freesurfer inherent striatal parcellations are so well fitted to even my severe AD patients, so I was hoping I could somehow adapt this to the Choi ROIs.

On Wed, Jun 18, 2014 at 8:45 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Paul

Thomas Yeo (ccd) would be the best person to help you, but he may not be reading email for a while....

cheers Bruce

On Wed, 18 Jun 2014, Paul Beach wrote:

Hi Freesurfers,

...

My processing stream involves moving the parcellated functional networks of Yeo and Choi to original subject domain to do connectivity analyses. While my process works very well for the Yeo networks I'm rather unsatisfied by the results of the Choi translations.

I'm hoping someone has some suggestions for improving things so that the Choi ROIs map onto individual subjects nearly as well as the general Freesurfer striatal segmentations.

NB - I work with AD patients, so I'm sure part of the problem is atrophy-based. However, I'm sure there are ways to improve things...

My current pipeline involves two steps: mri_vol2vol \ --mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \ --o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp nearest

mri_label2vol \ --seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \ --reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \ --invertmtx \ --o Choi_17Network_tight_striatum_orig.nii.gz \ --temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz

I suspect one way to improve things would be to do a recon-all based procedure, but I have no clue what commands within the recon-all domain that would involve.

Thanks for your suggestions.

Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program - MSU Cognitive and Geriatric Neurology Team

(CoGeNT)

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