It appears that Email in Plaint Text makes the command line look ugly. Here is
a cleaner view. These two should provide the right amygdala as the anatomical
ROI in MNI152 2mm space.
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
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I
generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve"
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> wrote:
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<mailto: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<mailto: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<mailto: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<mailto: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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