Sorry, what are you trying to do with that vol2vol command? The command
line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote:
> 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" <fis...@nmr.mgh.harvard.edu> 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" <yung-jui.y...@yale.edu>
>>> 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" <fis...@nmr.mgh.harvard.edu>
>>>> 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" <yung-jui.y...@yale.edu>
>>>>> 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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