Sorry, I've lost track of what is going on here. How was

lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz

created?


On 7/23/15 12:08 PM, Barbour, Tracy,M.D. wrote:
> Thank you Doug
>
> I tried the way you suggested and the registration actually looks worse. I 
> also tried:
>
> mri_label2vol --subject fsaverage --label 
> /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage_copy/label/$label.label
>  --o $TARGET_DIR/tracy2_$label.nii.gz --reg 
> $FREESURFER_HOME/average/mni152.register.dat --temp 
> /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz
>
> Is there a step that I am missing? This is for an amygdala functional ROI 
> that was created in tkmedit and saved as a label.
>
> Tracy
>
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, July 20, 2015 2:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] bad registration using mri_vol2vol
>
> where did lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz come from?
> It must be in the space of $SUBJECTS_DIR/fsaverage/mri/orig.mgz for that
> transform to work
>
> On 07/17/2015 02:43 PM, Barbour, Tracy,M.D. wrote:
>>
>> Hello,
>>
>> I'm trying to convert an ROI mask I created in MNI305 space to MNI152.
>> After running MRI_vol2vol the registration looks off (too anterior).
>>
>> Here are my commands:
>>
>> mri_convert -ot nii lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz
>> lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii
>>
>> mri_vol2vol --mov
>> /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz
>> --targ lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii --inv
>> --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat
>> --o new_lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii.gz
>>
>> Any ideas why the registration is off?
>>
>> Tracy
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
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>

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