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 <fis...@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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--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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