Thomas,
Thank you so much for this input. I tried out both the striatum and the
general MNI152 template. For the striatum the match is *SO* much better.
The MNI152 template also looks alright - though it's a little fuzzy.
I'm pretty happy with this now and I'll definitely have more confidence in
any striatum-based connectivity differences I see now.
Thanks again.
Paul
On Thu, Jun 19, 2014 at 11:07 AM, Thomas Yeo <thomas....@nus.edu.sg> wrote:
> Sorry for the slow reply. Here's a (non-ideal) suggestion:
>
> 1) Assuming you are quite happy with the freesurfer striatal parcellation
> in your AD subjects, then I am assuming freesurfer nonlinear registration
> (talairach.m3z) is working quite well. Talairach.m3z warps your subject to
> an internal freesurfer space (kinda like MNI305, but not quite). Let's say
> the freesurfer recon-all output is at <something>/AD_SUBJECT_FS/
>
> 2) Run the MNI152 1mm template (the one from FSL) through recon-all.
> Recon-all will give you a Talairach.m3z that allows you to map the MNI152
> 1mm template to the internal freesurfer space. Let's say the freesurfer
> recon-all output is at <something>/MNI152_FS/
>
> 3) Then do the following:
>
> a) Use mri_vol2vol to upsample the Choi striatal atlas which is 2mm
> resolution to the 1mm MNI152 template:
>
> >> mri_vol2vol --mov Choi_atlas.nii.gz --targ MNI152/mri/norm.mgz
> --regheader --o Choi_atlas1mm.nii.gz --no-save-reg --interp nearest
>
> Notice that I use norm.mgz of the MNI template rather than the original
> MNI template? norm.mgz is the 256 x 256 x 256 conformed version of the MNI
> template that recon-all puts through.
>
> b) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>
> >> setenv SUBJECTS_DIR <something>
> >> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
> Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
>
> c) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
>
> >> setenv SUBJECTS_DIR <something>
> >> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
> AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z
> talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph
>
>
> This is not optimal because of the double interpolation. You might want to
> use the MNI template instead of the Choi_atlas to test the above, so you
> can check the goodness of the warp. The final warped MNI template should
> hopefully look identical to your AD subject. If that works, then use the
> Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z
> below version 5, so you should use version 5x mri_vol2vol.
>
> --Thomas
>
>
>
>
>
>
>
>
>
> On Wed, Jun 18, 2014 at 10:04 PM, Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>> Hi,
>> The recon-all based striatal parcellations are based on the anatomy of
>> each particular subject, guided by a probabilistic atlas. That is
>> inherently likely to be more accurate that just taking a set of
>> ROIs/parcellations defined in some (non-probabilistic) atlas and warping
>> them to each subject via an affine transformation, which is what it sounds
>> like you are doing with the "Choi ROIs".
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> -----------------------------------------------------------
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO 63110 Email: mha...@wustl.edu
>>
>> From: Paul Beach <pabea...@gmail.com>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Wednesday, June 18, 2014 8:52 AM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Cc: Thomas Yeo <thomas....@nus.edu.sg>, "Yeo, Boon Thye Thomas -- Boon
>> Thye Thomas Yeo" <ytho...@csail.mit.edu>
>> Subject: Re: [Freesurfer] Fwd: Improving translation of Choi striatal
>> ROIs to original domain
>>
>> 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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>>>
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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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>
--
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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