6 Feb
2013
6 Feb
'13
8:05 p.m.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <pabeach1@gmail.com <mailto:pabeach1@gmail.com> <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> wrote: Thanks for your help! On Tue, Jan 22, 2013 at 11:12 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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. 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Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
greve@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/