Hi, I just wanted to post back the problem was solved (Thanks Doug). The solution is this:
1. use mri_aparc2aseg mri_aparc2aseg --s $SUBJECT --o <filename>.mgz --annot <annot_name> --annot-table <clut_file> [Note, in my case I was using 3 different values, 1, 2, 3 for the labels with only left hemisphere labels (the details will change for people with different label numbers etc.)] 2. read in the resulting file (python or matlab: pick your poison). set all voxels less than 1001 to 0, set all voxels greater than 1003 to 0, remap voxels with value 1001 to 1, 1002 to 2 1003 to 3. Now you are done and can load with your clut file. hth d On Mon, Feb 29, 2016 at 2:16 PM, dgw <dgwake...@gmail.com> wrote: > Hi, > > I just wanted to repost this question. After turning on the > transparency, I also noticed that this problem goes both directions > (i.e. some voxels which aren't gray matter in the lh.ribbon.mgz are > labeled utilized when calling mri_label2vol. > > On Tue, Feb 23, 2016 at 3:19 PM, dgw <dgwake...@gmail.com> wrote: >> Hi, >> >> I am having trouble with the projfrac option in mri_label2vol (on the >> current dev freesurfer environment). When I use the following command: >> >> mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o >> lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1 >> .01 >> >> I get many missed voxels from the gray matter (see the attached image, >> with the yellow representing the label overlaid on the ribbon.mgz). I >> have tried more extreme delta values and this doesn't help. (note >> scrolling to nearby slices indicates the neighboring voxels are >> included, so it isn't from the angle projecting oddly (that is why I >> took a slice from the middle of this large label)). Is there a better >> way to convert the annotation to a volume just in the gray matter, but >> including all of the relevant voxels? >> >> Is there a fundamental algorithmic difference between mris_volmask and >> mri_label2vol? >> >> If yes, why? >> >> Thanks, >> D _______________________________________________ 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.
