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 $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the header information is different. Therefore the "regheader" flag takes care of that. --Thomas On Mon, Nov 11, 2013 at 7:40 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > Is the Choi2012 volume in fsaverage/mni305 space? If so, then the 2nd > command is the right one. Use mri_binarize with the --match option to > create separate masks. > doug > > > On 11/11/13 2:24 PM, Kathy L. Pearson wrote: >> To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I >> have tried both of the mri_vol2vol commands below. The results as shown in >> freeview are offset by several voxels from the original. Is there a >> transform or an intermediate step that can make this work -- or a different >> command? Also, is there a recommended way to extract each individual value >> (here 1 ... 7) to create separate masks in FSL 2mm space? >> >> Thanks for any advice, >> >> Kathy Pearson >> >> #!/bin/bash >> input=$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& >> >> _______________________________________________ >> 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
