The "annotation" is the name we give to a surface segmentation (eg, lh.aparc.annot). You can break lh.aparc.annot into its constituent label files. You can then replace the insula label file with posterior and anterior labels that you create. You can then recombine the labels back into a new annotation. Once you have the new annotation, you can run mri_aparc2aseg to map the annotation into the volume. This method will do better at filling in the cortical ribbon than mri_surf2vol or mri_label2vol.
doug On 01/16/2013 01:25 PM, Paul Beach wrote: > Hi Doug, > > Thanks a lot for the reply. I'm relatively new to freesurfer and it's > great to see such a helpful community. > > I'm a little fuzzy on what you mean with your second suggestion, > related to the manual ROI creation/export to AFNI. Could you explain a > bit more about creating "a new annotation and then run mri_aparc2aseg." > > First, I'm not sure what you mean by "new annotation." > > Second, my understanding is that mri_aparc2aseg normally deals with > ROIs in the LUT. However, looking at the wiki for this command, it > seems as though I can utilize my created label using the "--annot > argName" option. > How does this look: > mri_aparc2aseg --s [subj] --annot lh.aIns.label --o lh.aIns_aparc > > > Cheers, > Paul > > > > On Wed, Jan 16, 2013 at 10:56 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Paul, > > On 01/16/2013 10:27 AM, Paul Beach wrote: > > Hello, > > > > I have two issues, currently. > > > > First, I was wondering if it would be possible to create separate > > FSAverage brains for different subject groups. I am working with > > healthy seniors and various stages of Alzheimer's disease, so > doing so > > would be very helpful from the perspective of not conflating the > > differences in neuroanatomy between the these groups. One idea > we had > > was to create separate HOME directories for each group, but we > wanted > > to know if there was an easier way. I can't find anything in the > > interwebs about this. > You can create your own fsaverage subject using make_average_subject. > Note that when you run recon-all it registers to the standard > fsaverage > space. If you want to register to a different space, you will need to > re-run mris_register. Once you do this, you will not be able to > compare > groups. > > > > Second, I utilize some ROIs that are not specified by FS (such as > > secondary somatosensory cortex and anterior vs. posterior > insula). My > > means of getting around this was to use FSAverage and tksurfer to > > hand-draw them, save them as '.label' files, map them to individual > > subjects, and export them to AFNI since much of our correlation > > analysis is done on that platform. However, I've noticed that when I > > view these hand-drawn ROIs in AFNI they only show up at the > border of > > the gray and white matter, rather than filling the entirety of the > > gray matter. Note that this problem does not occur for ROIs in the > > look up table (like the caudal ACC). Exporting these to AFNI > gives you > > a nice ROI that fills all the gray matter in the defined region. > Try using --proj frac 0 1 .1 with mri_label2vol. Or you can create > a new > annotation and then run mri_aparc2aseg. The 2nd method works a little > better since the 1st method can leave some holes. > > doug > > > > _Code I'm using_: > > For the latter problem, what I first use is mri_label2label to > map the > > fsaverage-based ROI onto individual subjects, for example with the > > left anterior insula, before using mri_label2vol: > > *mri_label2label --srclabel lh.aIns.label --srcsubject fsaverage > > --trglabel lh.aIns.label --trgsubject [subj] --regmethod surface > > --hemi lh* > > > > *mri_label2vol --label ../label/lh.aIns.label --regheader > > aparc+aseg.mgz --o gmroi_volume.nii.gz --temp orig/001.mgz* > > > > > > Then I copy the new volume file to their AFNI folder, rename it, and > > run my correlation analysis on them. > > > > Note, that for those ROIs that are in the look up table (those > > parcellated by freesurfer) I simply use mri_label2vol before > > extracting them using 3dcalc (for example, the caudal anterior > > cingulate)... > > *mri_label2vol --seg aparc+aseg.mgz --regheader aparc+aseg.mgz --o > > gmroi_volume.nii.gz --temp orig/001.mgz* > > > > *3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1002)' -prefix > > ROI_FS_lh.caudalACC.nii.gz* > > > > > > > > tl:dr > > Is it possible to "easily" create multiple FSAverages based on > > selected subjects (in my case, subject groups separated by > disease state)? > > > > and > > > > Does anyone have any advice on how to get hand-drawn surface-based > > ROIs from Freesurfer's tksurfer into AFNI that full cover the > entirety > > of the gray matter? > > > > > > Cheers and thanks! > > -- > > Paul Beach > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM Chapter -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
