Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

autorecon1 error
by Xiangchuan Chen 03 Oct '07

03 Oct '07

Hi all, I have got the following error message when running "recon-all -autorecon1" with one of my subject's data: SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. ... recon-all exited with ERRORS at ... Could anybody tell me how to resolve this issue? Thanks in advance, Xiangchuan Chen

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Segmentation of MRI with cortical lesions
by Martti Ilvesmäki 02 Oct '07

02 Oct '07

Hi, I'm using Freesurfer to generate the necessary surface-files for MNE software. However, when using the automatic segmentation on MRI from patients with cortical lesions, the segmentation does not work correctly. In one case the pial matter surface forms a deep hole (several cm) into the cortex at the location of the lesion. In another case the generated pial matter surface runs approximately along the surface or the white matter and the generated white matter surface seems blurred, with no distinct connection to the anatomy. What would be the easiest way to correctly segment these images? Or is there no simple way? Thanks in advance, Martti Ilvesmäki

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loading surface as a weighted graph
by Michael Harms 02 Oct '07

02 Oct '07

Hello, This question is directed to the universe of FS users: Has anyone created a set of tools (e.g., Matlab) for converting FS surfaces into a (sparse) weighted graph structure? In principle, it doesn't seem like this will be too difficult to implement (making use of the some of the existing FS/Matlab 'read' functions that are already available). But, if anyone already has existing code that they are willing to share, I'd appreciate hearing from you. cheers, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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RE: [Freesurfer] automated parcellation: training set of Freesurfer
by "Woo Suk, Tae" 02 Oct '07

02 Oct '07

Dear Dr Bruce Fischl. How are you? I preprocessed 41 subjects' MRI to measure the volumes of the cortical and subcortical structures with ver 3.04 Freesurfer. What kind of atlas (Desikan-Killiany atlas or Destrieux atlas?) was used for my data? And how can I choose the atlas between the two atlases. If you provide me the tool for new training set, I'd like to create my own study specific atlas. Really thank for your reply! Sincerely Woo Suk, Tae -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 9:03 PM To: Woo Suk, Tae Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] automated parcellation: training set of Freesurfer there are two training sets we use for the two difference parcellation schemes. Once consists of about 40 subjects distributed into 4 groups (young, middle aged, elderly and Alzheimer's for the Desikan-Killiany atlas). The other is 14 young and middle aged subjects in the Destrieux atlas. Defining a new training set is extremely labor intensive, but we distrubute tools for you to do so if you decide to. cheers, Bruce On Mon, 1 Oct 2007, Woo Suk, Tae wrote: > Dear experts. > > In the previous technical papers of Freesurfer, the the method of automated parcellation was described, > > "This procedure automatically assigns a neuroanatomical label to each voxel > in an MRI volume based on probabilistic information automatically estimated > from manually labeled training set." > > I'd like to know more detail, how many training set was used in Freesurfer, > and is it possible to define the study specific training set for automated parcellation using Freesurfer? > > Sincerely > > Woo Suk, Tae > Seoul, Korea > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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significance in unknown region
by Kirk, Gregory 01 Oct '07

01 Oct '07

Hi All, I have wondered what is done in the medial and inferior region where a patch needs to be put across to seal each of the two hemispheres. The variables , thickness etc... have some value in the region as we see a representation on the thickness maps. Is something like averaging with a diffusion equation i.e. computing a distance weighted average of the border of the surounding real cortex performed ? thanks curious Greg.

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within group contrast vector
by Elizabeth Mormino 01 Oct '07

01 Oct '07

Hello. I am trying to do a within group analysis looking at the effect of cognitive performance on cortical thickness, controlling for age and gender. I only have one class declared and my variable of interest is listed as the first variable in the FSGD file (with age and gender second and third). Should my contrast vector look like this: 0 1 0 0 Thanks for you help! I have enjoyed using your software very much! Beth

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registration problem
by Robert Levy 01 Oct '07

01 Oct '07

Hi, I have 3 contrasts between conditions in a between group comparison on the volume, and I'm using mri_volcluster to get information about the data. For some reason, while two of the contrasts (ASvfix and ASevASc as shown below) are compatible with the register.dat file for these contrasts, one of the contrasts (ASevifx) is not compatible. I'm not sure why or how this could be the case, but I need to register it somehow, in order for the talairach coordinates to be listed correctly. What do you think is wrong or different about this one contrast? Is there anything that I can do to fix this incompatibility so that it will register the correct coordinates? (detailed info for reproducing the problem is included below). Thanks, Rob To reproduce the problem: source /usr/local/freesurfer/nmr-dev-env # ( but I also get the same exact results using stable 3 ) setenv SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR cd $SUBJECTS_DIR # this contrast is not compatible with register.dat mri_volcluster \ --in BwGroupError5/bold/EMerror/tal-rfx/ASevfix/sig_000.bfloat \ --thmin 3.230014 \ --reg BwGroupError5/bold/EMerror/tal-rfx/register.dat \ --frame 6 # these 2 contrasts work mri_volcluster \ --in BwGroupError5/bold/EMerror/tal-rfx/ASvfix/sig_000.bfloat \ --thmin 4.668773 \ --reg BwGroupError5/bold/EMerror/tal-rfx/register.dat \ --frame 6 mri_volcluster \ --in BwGroupError5/bold/EMerror/tal-rfx/ASevASc/sig_000.bfloat \ --thmin 3.524190 \ --reg BwGroupError5/bold/EMerror/tal-rfx/register.dat \ --frame 6 -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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XYZ coordinates of vertices within aparc labels
by Juranek, Jenifer 01 Oct '07

01 Oct '07

I'd like to retrieve information wrt XYZ coordinates of vertices within aparc labels. I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?) Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc 1) What is the name & location of the table file I should be specifying to return all 94 labels? Or do I need to include additional flags in my command line? 2) How are the columns ordered within each output file generated by the mri_annotation2label command? I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir. Many Thanks, Jenifer

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averaging scans
by Sarah J Greene 01 Oct '07

01 Oct '07

Hi all, I have a question about averaging scans. We are trying to average 2 scans taken one after another on the same person to run them through FreeSurfer, but are not sure of the command to do this. Does anyone know of the command, and at what point in processing to use it? Thanks! sarah

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question why mri_aparc2seg would fail?
by Turner, Jessica 01 Oct '07

01 Oct '07

Dear FS experts, We have a situation where mri_aparc2seg is failing on some subjects but not others. Since the processing on all the subjects up to this step was the same, we're trying to figure out the problem. We're using version 3.05 on a linux system. Here is the log: ***************************** mri_aparc2aseg failing log ********************* mri_aparc2aseg --s 000981972381 --a2005s SUBJECTS_DIR subject /phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/00098197 2381 outvol //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/0009819 72381/mri/aparc.a2005s+aseg.mgz useribbon 0 baseoffset 100 Reading lh white surface //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/0009819 72381/surf/lh.white Building hash of lh white Reading lh pial surface //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/0009819 72381/surf/lh.pial Building hash of lh pial Loading lh annotations from //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/0009819 72381/label/lh.aparc.a2005s.annot reading colortable from annotation file... colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_lab els2005.txt) Reading rh white surface //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/0009819 72381/surf/rh.white Building hash of rh white Reading rh pial surface //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/0009819 72381/surf/rh.pial Building hash of rh pial Loading rh annotations from //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/0009819 72381/label/rh.aparc.a2005s.annot reading colortable from annotation file... colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_lab els2005.txt) Have color table for lh white annotation Have color table for rh white annotation Loading aseg from //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/0009819 72381/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 ERROR: could not map to any surface. crs = 121 137 152, ras = 7.0000 24.0000 -9.0000 what's that indicate? Many thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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