Hi Doug, the Choi volume is in MNI152 space, not MNI305 space.
Hi Kathy, the correct command is "mri_vol2vol --mov $input --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o output1.nii.gz --no-save-reg --interp nearest"
Please note the use of the "--regheader" flag. The Choi volume is in exactly the SAME space as the $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the header information is different. Therefore the "regheader" flag takes care of that.
--Thomas
On Mon, Nov 11, 2013 at 7:40 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Is the Choi2012 volume in fsaverage/mni305 space? If so, then the 2nd command is the right one. Use mri_binarize with the --match option to create separate masks. doug
On 11/11/13 2:24 PM, Kathy L. Pearson wrote:
To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I have tried both of the mri_vol2vol commands below. The results as shown in freeview are offset by several voxels from the original. Is there a transform or an intermediate step that can make this work -- or a different command? Also, is there a recommended way to extract each individual value (here 1 ... 7) to create separate masks in FSL 2mm space?
Thanks for any advice,
Kathy Pearson
#!/bin/bash input=$FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152/Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz mri_vol2vol --mov $input --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o output1.nii.gz --no-save-reg --interp nearest --precision uchar mri_vol2vol --targ $input --mov $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --inv --reg $FREESURFER_HOME/average/mni152.register.dat --o output2.nii.gz --no-save-reg --interp nearest --precision uchar
# Compare results freeview $input output1.nii.gz output2.nii.gz&
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