Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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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How to reorient brains collected headfirst prone
by Carl Anderson 01 Oct '07

01 Oct '07

Dear Freesufers, How do I preprocess for freesurfer, heads collected headfirst prone instead of the normal headfirst supine? Thanks, Carl ------------------------------------------------------- Carl M. Anderson, Ph.D. Assistant Professor of Psychiatry, Harvard Medical School & The Brain Imaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972 Fax: 617-855-2770 webpages: http://remfractal.mclean.org/main.html email: carl_anderson(a)hms.harvard.edu ------------------------------------------------------- Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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Re: [Freesurfer] convert mnc->analyze->mgz
by Olivier Coulon 01 Oct '07

01 Oct '07

Hi everyone, >> but then, when I do mri_convert -it analyze -i subject -o subject.mgz, >> the volume is shifted to one side (in addition to left/right swapped). >> If you look at the coronal sections I'm attaching, you see that a >> piece of ear the right ear is appearing at the left. I also have this problem of left/right inversion and I cannot figure out why this happens. Do we have to specify a --out_orientation string ? Thanks, Olivier -- --------------------------------------------------------------- Olivier Coulon, Chargé de Recherche CNRS Laboratoire LSIS, UMR CNRS 6168 Equipe I&M, ESIL Campus de Luminy - Case 925, 13288 Marseille cedex 09 - France Tél: +33 (0)4 91 82 85 27 Fax: +33 (0)4 91 82 85 51 email: olivier.coulon(a)univmed.fr http://olivier.coulon.perso.univmed.fr ---------------------------------------------------------------

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automated parcellation: training set of Freesurfer
by Woo Suk, Tae 01 Oct '07

01 Oct '07

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

2 1

convert mnc->analyze->mgz
by roberto toro 29 Sep '07

29 Sep '07

(sorry. I just clicked reply, and didn't send the screenshots to the list) You can see in the images (I'm using neurolens) the contraction of the left-right axis and the shift: the black space at the left and right sides is even originally but uneven in the converted data. In another slice (not included) you can see a little bit of the right ear appearing from the left side. There's also the problem with the rotation, the nose is originally pointing to the right but then it's pointing down, which is why the axial slices look coronal and vice-versa. Keeping that in mind, you can see that left and right hemispheres are swapped (look at the shape of the posterior horn of the ventricles, which is longer in the left hemisphere) thanks, roberto ---------- Forwarded message ---------- From: roberto toro <rtoro(a)snv.jussieu.fr> Date: Sep 27, 2007 4:23 PM Subject: Re: [Freesurfer] convert mnc->analyze->mgz To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> On 9/27/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Roberto, > > can you send us the command line and full screen output of the minc to > mgz step? It shouldn't change the aspect ratio. > > thanks, > Bruce hi Bruce, here's the command: roberto% mri_convert P.mnc P.mgz mri_convert P.mnc P.mgz reading from P.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to P.mgz... roberto% and I attach screenshots of the result (which is scaled and shifted). thank you, roberto

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Simple_Surface_labels2005.txt
by Juranek, Jenifer 28 Sep '07

28 Sep '07

I'd like to identify the voxel locations of each vertex within each aparc label. I found the command "mri_annotation2label" and thought it might do the trick. However, I noticed that the examples http://surfer.nmr.mgh.harvard.edu/fswiki/mri_5fannotation2label?action=h ighlight&value=mri_annotation2label refer to a txt file which I do not seem to have in my $FREESURFER_HOME dir. While the table specified in the examples is <Simple_surface_labels2005.txt> I only seem to have <surface_labels.txt> which appears to have 95 lines of text. Using the surface_labels.txt file yields only 12 files rather than the expected 94. 1) Is strategy appropriate? 2) Which file should be specified with the -table flag? 3) Best guess as to where to find the proper file to be specified with the -table flag? Many Thanks for any assistance you can provide... Jenifer

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