Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following
commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz
--o right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o
right_amygdala.nii.gz
rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain
a similar file in MNI152 1mm space, based on
${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a
1mm file?
Best,
Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <[email protected]> wrote:
>mri_vol2vol with the transforms/talairach.xfm as the transform should do
>the trick. Make sure that the resample type is nearest neighbor
>
>Cheers
>Bruce
>
>> On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <[email protected]>
>>wrote:
>>
>> Hi Bruce,
>>
>> Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very
>> flexible. I meant to obtain the aseg individual label files in MNI152
>> space as NIfTI files, for example, the different parts of the CC.
>>
>> Could you please point me to the right direction, as to what tool I
>>should
>> use for this purpose (preferably a command line tool, rather than a
>> visualization tool)?
>>
>> Best,
>> Daniel
>>
>>> On 6/15/14, 10:16 PM, "Bruce Fischl" <[email protected]>
>>>wrote:
>>>
>>> Hi Daniel
>>> Any of our tools can write nifti if you give the output volume the
>>> extension .nii or .nii.gz
>>>
>>>
>>> Cheers
>>> Bruce
>>>
>>>> On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <[email protected]>
>>>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> While it is possible to obtain NIfTI files for cortical parcellation
>>>> using mri_annotation2label, I am running if it is possible to obtain
>>>> NIfTI files associated with aseg parts?
>>>>
>>>> Thanks!
>>>> Daniel
>>>>
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