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30089 discussions

mri_annotation2label problem
by mnd12＠nmr.mgh.harvard.edu 13 Aug '12

13 Aug '12

Hello, I'm attempting to use a custom parcellation scheme (Lausanne2008) on fsaverage5. The gcs files I'm using can be found here: https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs/my_atla… The problem I'm getting is when I run mri_annotation2label using the annotation files I create using these gcs files and lh.sphere.reg I noticed that some of the labels are not being extracted, as seen in the first few lines of output copy/pasted here: 0 820 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.unknown.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.unknown.label 4 190 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.corpuscallosum.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.corpuscallosum.label 6 30 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.entorhinal_1.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.entorhinal_1.label so it appears to skip labels 1,2,3 and 5. Interestingly this problem is only occurring when I use the gcs files named P1_16 P17_28 P29_36. Also, I'm able to successfully use this parcellation scheme on other subjects and with fsaverage, just not fsaverage5. Any help would be greatly appreciated! Thanks in advance, Matt DeSalvo

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3d Gaussian filter on volume
by John Papaioannou 13 Aug '12

13 Aug '12

Hi, I can run a 3d Gaussian spacial filter on a T1.mgz image using matlab functions, but I was wondering if there isn't already a freesurfer script that does the same (with a FWHM input). John ___ John Papaioannou Medical Imaging Sciences Digital Mammography, CAD Mammography Department of Radiology Biological Sciences Division The University of Chicago 5841 South Maryland Avenue Chicago, Illinois 60637 773.834.5104 voice 773.702.0371 fax

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mris_fix_topology stops with two T1-s
by Garikoitz Lerma Usabiaga 13 Aug '12

13 Aug '12

Hi FS experts, I've run recon-all -i file -s subject -qcache -measure thickness -all to: - 18 subjects, session 1 T1 - same 18 subjects, session 2 T1 and everything went well. Then I copied the <subject_id_session>/mri/orig/001.mgz-s to <subject_id>/mri/orig/001.mgz and 002.mgz, and run the same command again: recon-all -s <subject_id> -qcache -measure thickness -all Half of the subjects are failing when trying to correct the topology. Please find below the outputs of two of the subjects. Should I use the -i and the original files instead of the already created 001.mgz files? What should I check in order to avoid this error or what should I do in order to correct it? thank you very much, Gari ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-956 (nv=167898, nf=337708, ne=506562, g=479) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 127705 ambiguous faces found in tessellation segmenting defects... 125 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 1 -merging segment 9 into 1 -merging segment 21 into 1 -merging segment 24 into 1 -merging segment 26 into 1 -merging segment 29 into 1 -merging segment 44 into 1 -merging segment 56 into 1 -merging segment 2 into 1 -merging segment 65 into 1 -merging segment 67 into 1 -merging segment 71 into 1 -merging segment 4 into 1 -merging segment 12 into 1 -merging segment 34 into 18 -merging segment 30 into 19 -merging segment 38 into 35 -merging segment 61 into 47 -merging segment 107 into 106 -merging segment 115 into 113 105 defects to be corrected 0 vertices coincident reading input surface /home/BCBL/glerma/freesurfer/subjects/BERTSO/B_16/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -7.9838 (-3.9919) -vertex loglikelihood: -5.7349 (-2.8674) -normal dot loglikelihood: -3.5106 (-3.5106) -quad curv loglikelihood: -6.1770 (-3.0885) Total Loglikelihood : -23.4063 CORRECTING DEFECT 0 (vertices=23, convex hull=21) After retessellation of defect 0, euler #=-32 (96640,274187,177515) : difference with theory (-102) = -70 CORRECTING DEFECT 1 (vertices=44927, convex hull=14482) Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-600 (nv=159708, nf=320616, ne=480924, g=301) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 115040 ambiguous faces found in tessellation segmenting defects... 96 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 16 into 0 -merging segment 39 into 0 -merging segment 48 into 0 -merging segment 22 into 21 -merging segment 38 into 34 -merging segment 42 into 37 -merging segment 70 into 69 89 defects to be corrected 0 vertices coincident reading input surface /home/BCBL/glerma/freesurfer/subjects/BERTSO/B_11b/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -7.9998 (-3.9999) -vertex loglikelihood: -5.5541 (-2.7771) -normal dot loglikelihood: -3.5423 (-3.5423) -quad curv loglikelihood: -6.1041 (-3.0520) Total Loglikelihood : -23.2003 CORRECTING DEFECT 0 (vertices=41794, convex hull=12626)

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Displaying cortical thickness changes in volume images
by Rajagopalan, Venkateswaran 13 Aug '12

13 Aug '12

Dear All, I would like to display my cortical thickness chnages from longitudinal runs on my original T1-w volume images. I am wondering whether this is possible if so can anyone tell how I can do this. Thanks in advance Venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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(no subject)
by Hugh Pemberton 12 Aug '12

12 Aug '12

Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh

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Averaging overlays/labels across subjects
by raij＠nmr.mgh.harvard.edu 12 Aug '12

12 Aug '12

Dear Surfers, I have (non-fMRI) .w format surface overlays/labels, computed at the smoothwm surface in each individual subject, in 25 subjects. FS5.1 recon-all has been run for all T1 images. I already managed to convert all individual surface overlays into the surface space of one of the subjects (or fsaverage) using mri_surf2surf, and in the process also converted the format from .w to .mgh (as I understand .w is pretty much legacy). Now, I would just need to compute an average across these overlays. I would greatly appreciate any suggestions which FS tools to use for this. Thank you in advance! (In case it matters, the overlays are E-field estimates, with a numerical value given for each vertex point. Also each overlay has only one time point.) Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Re: [Freesurfer] Tracula question
by Anastasia Yendiki 10 Aug '12

10 Aug '12

Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is "bet" - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez wrote: > The required files were not generated. > > the error occurs at > > rh.slft_PP_roi2.flt.nii.gz --bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain > _mask.flt.nii.gz --fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl > t.nii.gz --ncpts 5 --trunc --debug > ERROR: fio_pushd: > /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni > ERROR: Must specify brain mask volume for output subject > > does the brain mask have to be input manually in the configuration file, or > is this part of the pre-processing? since I set the bet thr to 0.23 in the > config file i thought the brain mask was also created during the > preprocessing stage. Attached is my log file. > > I am familiar with FSL but I am using Free surfer since i think automating > the entire process, including tracking is a great advantage, but I'm just > starting to get the hang of it > > Thanks! > > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement Sciences Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > dtifit_FA.fl > t.nii.gz > > > >

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BOLD vol2surf dimension mismatch
by Linda Douw 10 Aug '12

10 Aug '12

Hi all, I'm trying to project volume BOLD time series to native surface in some subjects. First, I registered the functional data to orig.mgz, using: bbregister --s subj --mov func.nii.gz --reg register.dat --init-fsl --bold --o output.nii.gz The results look good in tkregister2. Then, I want to go from volume to surf, doing: mri_vol2surf --mov functional.nii.gz --reg register.dat --regheader nmr00524_FS --hemi lh --o /folder/ However, it gives this error message: Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 26361 Writing to /folder/ Dim: 132698 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (132698, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure I should probably use mri_vol2vol first, but which target volume should I then use? Or is there something else I'm doing wrong? Thanks for your help! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

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Re: [Freesurfer] WM-hypointensities
by Mary Ellen Koran 10 Aug '12

10 Aug '12

Hi, I'm responding to this archived email: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023599.html Is it possible to run recon-all with the switch -nowmsa to get rid of the white matter segmentation analysis? Thanks! > > Mary Ellen Koran > MD/PhD Candidate, MSTP > Thornton-Wells Lab, Center for Human Genetics Research > Vanderbilt University School of Medicine > Duke University, Class of 2009, BSE > Cell: 919.943.5114 > >

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Tracula question
by Natalia Sánchez 10 Aug '12

10 Aug '12

Hi! I am running tracula for the first time and I am encountering the following error: Loading brain mask of output subject from /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain_mask.flt.nii.gz niiRead(): error opening file /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain_mask.flt.nii.gz Loading FA map of output subject from /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.flt.nii.gz niiRead(): error opening file /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.flt.nii.gz Segmentation fault Darwin dhcp-165-124-9-95.phystherapy.northwestern.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Fri Aug 10 16:19:17 CDT 2012 what file is lowb_brain_mask.flt.nii.gz? should this have been created during tracula or is this file my nodiff image? Thanks! *-- Natalia Sánchez * PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611

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