Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

Problems with corrected Talairach transform
by Tali Swisher 21 Apr '11

21 Apr '11

Hi there, I recently tried to process a scan with v4.0.5, and it failed while checking the Talaraich transform. I manually fixed the transform using the tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach) and saved it, but I'm confused about how to proceed. The tutorial seems to say to rerun it from scratch, but I'm not clear on how to get it to use the corrected transform since I thought that rerunning it as written in the tutorial would overwrite everything. How do I incorporate the corrected transform I made into the usual recon-all commands? Thanks, Tali -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

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Workshop on Diffusion Tensor Imaging in San Francisco on June 7, 2011 (fwd)
by Bruce Fischl 21 Apr '11

21 Apr '11

FYI ---------- Forwarded message ---------- Date: Wed, 20 Apr 2011 15:49:41 -0700 From: "Weiner, Michael" <Michael.Weiner(a)ucsf.edu> To: "Weiner, Michael" <Michael.Weiner(a)ucsf.edu> Subject: Workshop on Diffusion Tensor Imaging in San Francisco on June 7, 2011 To everyone interested in MRI: We are organizing a workshop entitled "DIFFUSION IMAGING: Theory, Methods and Clinical Research Applications" on Tuesday, June 7, 2011, to be held at the UCSF Mission Bay Campus. We believe that this will be highly informative and please come if you are interested, and please pass this email on to anyone you know who might be interested. Michael W. Weiner, M.D. Director, Center for Imaging of Neurodegenerative Diseases (CIND) http://www.cind.research.va.gov/ San Francisco VA Medical Center 4150 Clement Street (114M), San Francisco CA, 94121 USA Professor of Medicine, Radiology, Psychiatry, and Neurology University of California, San Francisco, USA Principal Investigator: Alzheimer's Disease Neuroimaging Initiative (ADNI) http://www.adni-info.org/ Principal Investigator: Resource for MRI of Neurodegenerative Diseases http://www.rrmind.research.va.gov/ Scientific Data Sharing Project http://scientificdatasharing.com/ Tel: (415) 221-4810 x 3642, FAX (415) 668-2864 In Emergency pager is (415) 302-0590

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problem with mri_surfcluster
by Elizabeth Gutierrez 21 Apr '11

21 Apr '11

Hi all, We're trying to create labels from a group level sig.mgh file. However, after the labels are created and an annotation file/color table is made, we try to view the sig.mgh file and the annotation file in tksurfer, but they don't extactly overlap, even though they are both configured to the same threshold (min-2 max-5). Most of the labels are fine, but the labels closest to the the higher end of the threshold end up being hollow, and only outline the sig.mgh clusters instead of being completely filled out. Does that make sense? Here is our command for mri_surfcluster: mri_surfcluster --in sig.mgh --hemi lh --subject fsaverage --thmin 2 --thmax 5 --sign pos --no-adjust --cwsig --o ./output_id --ocn ./cluster_number --olab ./grouplabel Thanks in advance! Elizabeth -- Elizabeth C. Gutierrez Graduate Student Department of Brain and Cognitive Sciences Massachusetts Institute of Technology

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Selxavg3-sess error
by Wetherill, Reagan 21 Apr '11

21 Apr '11

Hello FreeSurfers! I am new to FSFast and am attempting to run selxavg3-sess, but I keep receiving the following errors: ERROR: model ??? In an assignment A(:) = B, the number of elements in A and B must be the same. Error in ==> fast_ldanaflac at 391 flac.ev(nthev) = flac_ev_parse(tline); Error in ==> fast_selxavg3 at 45 flac0 = fast_ldanaflac(analysis); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Here are my commands for mkanalysis and mkcontrast # FSBUILD freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.3 2010/07/30 16:51:11 greve Exp $ # MKACMD /usr/local/freesurfer5/fsfast/bin/mkanalysis-sess -a try -mni305 2 -fwhm 6 -event-related -p vwm.par -TR 2 -nc 3 -spmhrf 0 -refeventdur 4 -polyfit 2 -hpf .08 -nskip 4 -nuisreg wm.dat 3 -nuisreg vcsfreg.dat 3 -nuisreg global.waveform.dat 1 -mcextreg -fsd bold # DATE Tue Apr 19 12:17:42 PDT 2011 analysis try mcstem fmcpr fsd bold TR 2 RegDOF 6 RawSpace volume mni305 2 mask brain RawFWHM 6 RawSTC none inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 4 polyfit 2 HPFCutoffHz .08 nconditions 3 parname vwm.par RefEventDur 4 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay 0 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 nuisreg wm.dat 3 nuisreg vcsfreg.dat 3 nuisreg global.waveform.dat 1 nuisreg mcprextreg 3 mkcontrast-sess -analysis try -contrast six-v-two -a 3 -c 1 selxavg3-sess -sf sess_test -analysis try THANKS IN ADVANCE!! Reagan Reagan Wetherill, Ph.D. Postdoctoral Fellow Department of Psychiatry University of California, San Diego 8950 Villa La Jolla Drive. Suite C213 San Diego, CA 92037-0862 Phone: 858-822-3400 Fax: 858-822-3933

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tksurfer tool
by Man Xu 21 Apr '11

21 Apr '11

Hi everyone! When I use tksurfer to load surfaces, it takes around 7 minutes. Is this too long? I used "nmrenv" version of FreeSurfer. Thanks in advance for your help! Best, Karen

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PHILIPS DATA
by ana ;osp 21 Apr '11

21 Apr '11

Hello all- We are trying to do preprocessing on data collected with a Philips scanner. We could not make unpacking step work. Instead, we converted the dcm files for a run of interest using mri_convert and created a nifti file. We placed this file under Applications/freesurfer/sessions/<project>/<subject>/bold/001 directory. So when we run preproc-sess -s < subject > -fwhm 5 We get: ERROR: You must specify -per-run or -per-session When we run preproc-sess -s < subject > -fwhm 5 -per-run We get: -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects /Applications/freesurfer/sessions/< project > /Applications/freesurfer/fsfast/bin/preproc-sess -s < subject > -fwhm 5 -per-run Wed Apr 20 16:10:32 EDT 2011 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain <subject> Template ----------------------------- mktemplate-sess -s < subject > -d /Applications/freesurfer/sessions/<project> -fsd bold -update Session: /Applications/freesurfer/sessions/< project >/< subject > ---------------- Wed Apr 20 16:10:32 EDT 2011 find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found Does anyone know how to fix this problem? Thank you very much Ana

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Visualize contacts inside brain volume with overlay image
by Gabriele Arnulfo 21 Apr '11

21 Apr '11

Dear freesurfer experts, I was wondering if there's an easy way to visualize contacts of intra-cerebral electrodes within tkmedit. Here's the scene: I've got a volume, which contains a white cross for each contacts on some linear intra-cerebral electrodes. This volume is in nifti format. I'd like to visualize it as an overlay to the orig volume and add also pial border in order to identify which contacts lay in white matter and which ones not. I've tried adding the nifti voulme as a functional overlay but I cannot see anything maybe is only a setting problem for the color-scheme. I've tried to modify the settings inside the View Menu for the functional overlay but nothing happen (maybe because it expects to have functional data not a binary mask). Is there an easy way to accomplish my task? Best regards, previously coregistered to orig.mgz, gabriele

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tkmedit and tkregister2 permission or ? problems
by jim kroger 20 Apr '11

20 Apr '11

Hello, I am having trouble running tkmedit and tkregister2. With tkregister2, I issue the command tkregister2 --mgz --s heinrick/mri/transforms/talairach.xfm --fstal (and sometimes I leave out the path, and sometimes I put /urs/local/freesurfer/subjects/heinrick....) always, though I am root and have chmodded eveything to 777, I get the error: ---- WARNING: cannot write to /usr/local/freesurfer/subjects/heinrick/mri/transforms/talairach.xfm/mri/transforms. You will not be able to save any edits. Hit Enter to continue: ... continuing regio_read_mincxfm: Not a directory ---- With tkmedit, I give this command and get the following error, and don't know where to start in fixing this problem: ---- tkmedit heinrick/mri/transforms/talairach.xfm heinrick/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/heinrick/mri/transforms/talairach.xfm/mri/heinrick/mri/brainmask.mgz, -1): could not open file Error: Loading volume heinrick/mri/brainmask.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. ---- I have used these before with no problem. I seem to suddenly have permission problems, or something. I don't know why tkmedit would not be able to open the brainmask file. Any help or pointers appreciated. Thanks, Jim Kroger -- Cell: 575-571-8274 Email: jkk251(a)gmail.com

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analysis questions
by Ilana Hairston 20 Apr '11

20 Apr '11

Hi there, 1. A followup question regarding contrasts in glmfit - when there are multiple contrasts, does that affect the degrees of freedom, or is each contrast tested separately? 2. When analyzing exported stats tables in SPSS, i can test hypothesis regarding specific regions without correcting for repeated measures across the whole brain. But the statistical power is much lower, and the volume or thickness is the average of the whole region, hence significant effects may not necessarily appear in glmfit. Is there a way of applying the glmfit to an ROI/label? thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

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Extracting LGI stats using a label file
by Robustelli, Briana (NIH/NIMH) [F] 20 Apr '11

20 Apr '11

Freesurfer team, I have run a group of subjects through the recon-all pipeline with the lgi option. I then looked at differences between two groups in qdec and ran a cluster correction. I would now like to extract the lgi statistics for 3 of these clusters. I have label files for these areas and tried using mris_anatomical_stats to calculate the lgi values. The script runs fine but does not appear to replace the cortical thickness values with lgi values. Below is the script I used to test it on subject "subj". Am I doing something incorrectly? Thank you. mris_anatomical_stats -l LGI_lh_001.label -t pial_lgi -f subj/stats/lh.aparc_lgi_cluster1.stats subj lh Briana -- Briana Robustelli Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C103 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 435-4491 Briana.Robustelli(a)nih.gov

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Freesurfer April 2011