Hi Doug, I see. It works well. Just curious, when should we use reg.2mm.mni152.dat then?
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? Thanks! Daniel From: Douglas Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right. Thanks, Daniel From: Douglas Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest doug On 6/16/14 3:13 PM, Yang, Daniel wrote: 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 <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> 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" <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! 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