Hi Paul, try this cd $SUBJECTS_DIR/youraveragesubjectname mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon youraveragesubjectname
doug On 02/04/2013 02:40 PM, Paul Beach wrote: > Hi Doug, > > Your suggestion to remove the 'unknown' label when using the > mris_label2annot command worked like a charm. Thanks! > > However, now I'm trying, as per your original advice, to re-run > mri_aparc2aseg in order to get my labels to fill out the entire > cortical ribbon (with the end goal of exporting these labels/ROIs to > AFNI). I tried this on my averaged subject (created with > 'make_average_subject') and it gave me the error that there is no > "ribbon.mgz" file in the mri folder. Upon checking the mri folder, > there is indeed no 'ribbon.mgz' file. > > Looking at the options for 'mri_aparc2aseg' on the wiki it doesn't > look like there's any way around this problem from that angle - at > least from the perspective of using my averaged subject. > > In the averaged subject's mri folder there are only the following files: > aseg.mgz > brain.mgz > orig.mgz > T1.mgz > brainmask.mgz > mni305.cor.mgz > p.aseg.mgz > > Interestingly, in the fsaverage subject there are ribbon.mgz files. Is > there a way to make a ribbon.mgz file for averaged subjects?? > > > Thanks, > Paul > > > > > On Thu, Jan 31, 2013 at 2:12 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Paul, this mostly looks right. I think the problem may be that > you are including the unknown label on the command line. I think > that mris_label2annot will ignore the 0 inthe ctab file, which > means that it assign the first label passed (lh.unknown.label) to > the the first non-zero ROI in the ctab file (banksts). Try that > and see if it works. > doug > > > On 01/30/2013 03:03 PM, Paul Beach wrote: > > Hi Doug, > > I've been attempting to utilize the programs suggested by you > to create manual labels (ROIs) on the cortical surface of > tksurfer to be able to export certain ones to AFNI. The > problem I was having originally was that the cortical ribbon > was not fully covered by surface drawn labels that were > changed to volumes by MRI_label2vol. > > You suggested first using mri_annotation2label to extract the > labels within the aparc.annot files (left and right > hemispheres), putting my created labels into the same folder > (replacing, for example, the "insula" label with anterior, > middle, and posterior insula labels) and then using > mris_label2annotation to make a new annotated file to be sent > into a re-ran mri_aparc2aseg. > > The problem I'm running into now, after extracting all the > labels, putting in my own, and running mris_label2annotis that > the resultant annotation's labels are highly out of place and > disorganized. For example, the label for the cuneus is where > the corpus callosum is. > > I'm wondering if this has something to do with the order of > labels in the mris_label2annot script of possibly with my > .ctab file. The latter was created based on what I found here > <https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit> > on the Freesurfer wiki. I simply added my six manual > labels/ROIs at the end. I tried to use their GWFSAnnotToLUT > > <https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit?action=AttachFile&do=view&target=GWFSAnnotToLUT> > program, but could not get it to work, so I'm not sure if the > .ctab file accurately represents tksurfer's Lookup Table. > > > I'm also not sure if it has something to do with overlapping > vertices of different labels. For example, will leaving the > "insula" label in mess things up when I also try to include > the anterior, middle, and posterior insula labels? If so, > would simply removing labels that overlap, vertex-wise, help? > > I have attached the setup of the .ctab file as well as my > mris_label2annot script. > > > Thanks for your advice, > Paul > > > On Tue, Jan 22, 2013 at 2:52 PM, Paul Beach > <pabea...@gmail.com <mailto:pabea...@gmail.com> > <mailto:pabea...@gmail.com <mailto:pabea...@gmail.com>>> wrote: > > Thanks for your help! > > > > On Tue, Jan 22, 2013 at 11:12 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > mri_annotation2label breaks them appart > mris_label2annot puts them back together again > doug > > On 01/22/2013 11:09 AM, Paul Beach wrote: > > Hi Doug, > > Thank you for this. However, can you give me a > hint as to > how I can go about breaking apart the aparc.annot > files > into their constituent label files? Are there a > particular > commands for doing this and eventually recombining the > labels into the overall aparc.annot file? > > > Thanks! > > > > On Wed, Jan 16, 2013 at 3:15 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: > > > 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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <http://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/ > > > > > -- 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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- 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 > > > > > -- > 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 <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/ > > > > > -- > 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
