Freesurfer January 2009

freesurfer@nmr.mgh.harvard.edu

72 participants
137 discussions

Qdec correlation analyses
by Xie, Hong 12 Jan '09

12 Jan '09

Hello, freesurfer group, I have run qdec for comparing thickness between two groups. When qdec does a correlation analyses for thickness versus a second variable: 1) Does the second variable have to be a continuous interval variable or 2) can the second variable be an ordinal variable with more than 2 levels? In the case of the correlation between two continuous variable, is the test a Pearson correlation? If 2) is possible, is the correlation a Spearman correlation? Thank for your help, Hong Xie

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Reusing ROIs
by Martin Kavec 12 Jan '09

12 Jan '09

Hi, For my group analysis I am thinking of reusing a specific set of cortical ROIs from already published data. I suppose that a target template (fsaverage) and ROIs itself should be sufficient to have. If I use the same fsaverage for my cohort, I should be able to get the data out of the ROIs of my subjects, and possibly compare it to the published results. Isn't it so? Thanks in advance for clarification, Martin

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retinotopy and alternating stimulus direction within-run
by Jeff Phillips 12 Jan '09

12 Jan '09

Hello all, I am wondering if the FS FAST retinotopy analysis can deal with within-run alternations of stimulus direction. I have collected data in which eccentricity and polar angle were manipulated in separate runs, but within each run, a cycle of stimulation in one direction was followed by a cycle in the opposite direction. For example, 32 s of clockwise-rotating wedges were followed by 32 s of counterclockwise wedges, etc. I realize now that this may not have been a wise choice--does FS FAST have some paradigm file option for alternating stimulation? If not, is my best solution to cut and splice my runs, dividing each into two mini-runs of single-direction stimulation? Thanks, Jeff

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(no subject)
by Gabriel GLZ 12 Jan '09

12 Jan '09

hello in the case that i have a ROI and i don't know wich voxeles are in there, or the coordenates of those voxeles, i want to create a specific label that only contains those voxeles, how can i do that??' _________________________________________________________________ Arrastrar y colocar: acceso muy fácil al uso compartido de fotos con Fotos de Windows Live™. http://www.microsoft.com/windows/windowslive/photos.aspx

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Sulcal depth measures
by Christine Ecker 12 Jan '09

12 Jan '09

Is there any way of measuring sulcal depth with FreeSurfer? Or is sulcal depth simply measured by the positive values in ?h.sulc - i.e. negative values are 'gyral heights' and positive values are 'sulcal depths'? If so is it possible to calculate these values for certain parcellated regions such as specific sulci in aparc? Thanks for your help!

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qdec X error of failed request
by Juranek, Jenifer 12 Jan '09

12 Jan '09

Hi, Running FSv405 on RHEL5. Recently obtained new error when qdec was attempted. Have successfully run qdec before on this box using FSv405. Only update made was to upgrade to FSLv412. Same error persists after restarting X. Both tkmedit and tksurfer work fine. Any ideas how to fix? Many Thanks, Jenifer [jjuranek@localhost subjects]$ qdec & [1] 4306 [jjuranek@localhost subjects]$ Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 66 (X_PolySegment) Serial number of failed request: 5529 Current serial number in output stream: 5532 [1] Exit 1 qdec

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accounting for BOLD response lag in FS retinotopy analysis
by Jeff Phillips 12 Jan '09

12 Jan '09

Hello all, I am performing my first retinotopy analysis, and I'd like to get some more information about the model created by paradigm files in the retinotopy analysis. Specifically, I am unsure whether to include or exclude fixation periods from the ends of my retinotopy runs. I imagine the analysis must somehow take into account the slow drop-off of the BOLD response--can you tell me if/how it does so? Since the analysis asks for the number of cycles, but not the duration of each cycle, I worry that including extra timepoints will just result in FS concluding that my stimulation period is longer than it actually is. If there exists an example design matrix for the retinotopy analysis, that would also be useful. Thanks, Jeff Phillips University of Pittsburgh

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fixing segmentation errors
by Jared Price 10 Jan '09

10 Jan '09

Hello freesurfers! We have a large data set which has segmentation volumes that have been manually labeled. Along the way occasionally a voxel which should have been labeled as left-hemisphere was labeled with the corresponding right-hemisphere label. For example, there might be a few voxels in the right putamen labeled as left putamen. Is there a quick fix for this? Thanks, Jared

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how is a path created?
by Michael Harms 09 Jan '09

09 Jan '09

Hello, I was wondering what approach is used to connect marked vertices when using the "Make Path" and "Make Closed Path" tools of tksurfer. Does the "connecting" operation just use the shortest (geodesic) distance between vertices, as determined by the currently displayed surface? Does the 'mri_path2label' binary use the same algorithm? And, is there any mechanism for taking curvature or sulcal depth into account? (e.g., connect points along a line of minimum or maximum curvature change, rather than using geodesic distance) thanks, 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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mri_surfcluster problem?
by Lauren LaCount 09 Jan '09

09 Jan '09

Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 10000 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like: mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_10000_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m fx_0.5frac_th01 --vwsig ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --cwsig /clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --o ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01 --ocn ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01 --olab ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01 (in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x) When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the "sum" file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 10000. Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere? Thank you! -Lauren -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Lauren LaCount Martinos Center for Biomedical Imaging Massachusetts General Hospital CNY 149, 13th St. Charlestown, MA 02129 llacount(a)nmr.mgh.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Freesurfer January 2009