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& > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
