Dear Doug,

I have problem similar to this:
I am trying to convert V1 labels from the Hinds method to volumes and transform them to MNI152 space for use in FSL. 
I tried using this command:
mri_label2vol --label rh.v1.prob.label --reg $FREESURFER_HOME/average/mni152.register.dat --temp MNI152_T1_2mm.nii.gz --o rh_v1_prob.nii.gz --label-stat rh_v1_prob_stat.nii.gz

...but the output is not registered correctly. It seems to be shift downward as Linda described.

Label conversion using the cmd  

mri_label2label --srclabel rh.v1.prob.label --s <subject> --regmethod surface --trglabel rh.v1.prob.new.label --hemi rh 

does not solve it.

Any suggestions?

Best regards,

Anders Hougaard

2011/10/18 Douglas N Greve <greve@nmr.mgh.harvard.edu>

The problem appears to be with the label itself. Try this conversion:

mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod
surface --trglabel lh.entorhinal.new.label --hemi lh

Also, you might want to use the entorhinal label define in the
aparc+aseg since it fills in the ribbon:
mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz
1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt

doug




Linda Douw wrote:
> Hi Doug,
> Thanks for the reply. This cmd makes it slightly better I guess, but still
> definetely off target. It seems to be shift downward, towards inferior,
> and therefore sometimes outside the skull. Any other ideas?
> Linda
>
>
>> The way the reg is set up, the targ is your mask. Try this cmd:
>> mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz
>> --o lh_entorhinal_MNI.nii.gz --reg
>> $FREESURFER_HOME/average/mni152.register.dat --inv
>>
>> doug
>>
>> Linda Douw wrote:
>>
>>> Hi all,
>>>
>>> I am trying to transform some labels from the aparc to masks in MNI
>>> space.
>>> Ideally, I would like to do this for each subject in my study
>>> individually
>>> (using their own rawavg.mgz and labels), but for now I started out with
>>> fsaverage. I first converted the label file into a nifti:
>>>
>>> mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject
>>> fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz
>>> --identity
>>>
>>> And then put the nifti file containing the label into MNI space:
>>>
>>> mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz
>>> --o lh_entorhinal_MNI.nii.gz --reg
>>> $FREESURFER_HOME/average/mni152.register.dat
>>>
>>> But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is
>>> completely wrong. I checked the location with tkregister as well:
>>>
>>> tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg
>>> /$FREESURFER_HOME/average/mni152.register.dat
>>>
>>> But here the entorhinal was also in the wrong place.
>>>
>>> Do you know how to fix this?
>>>
>>> Thanks,
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>>
>
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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