Hi Doug, I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space. Could you tell me which part is wrong? Thanks, Daniel From: Douglas Greve <[email protected]<mailto:[email protected]>> Reply-To: Freesurfer support list <[email protected]<mailto:[email protected]>> Date: Monday, June 16, 2014 at 8:16 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [Freesurfer] subcortical segment NIFTI files Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense doug On 6/16/14 1:38 PM, Yang, Daniel wrote: 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" <[email protected]<mailto:[email protected]>> 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" <[email protected]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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! 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