Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

some questions
by Siddharth Srivastava 20 Dec '08

20 Dec '08

Hi everyone, what is the difference in functionality between the mri_* commands and the mris_* commands? How does the mris_fill command maintain the distinction between the left and the right hemisphere? I see only one filled.mgz having 2 labels? does it write to the same file during each invocation (lh,rh), or just one call is enough to fill both hemispheres? mris_morphology: it is possible to specify the structuring element for the intended operation? best regards, sid

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Longitudinal processing , possible bias_shift ?
by Anthony 20 Dec '08

20 Dec '08

Hi all, Recently I tried out longitudinal processing on my 1st time point subjects ( directly generated by recon-all, no post processing or manual editing involved) . Then I ran asegstat2table for both 1st and 2nd time point subjects to compare cortical WM and cortical cortex volumes. From what I observed , there was possibly a bias_shift in WM between those time points as most of the differences ( WM at tp2 -WM at tp1 ) were positive , I was expecting the mean difference would be close to 0 . It would be great if anyone could share her/his insights about this .Is it normal and what might cause this behavior ? Thanks alot New Email names for you! Get the Email name you've always wanted on the new @ymail and @rocketmail. Hurry before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/

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4.1.0 on Ubuntu 8.04
by hashiryu 17 Dec '08

17 Dec '08

Dear all, I have installed the version 4.1.0 (centos x86_64) on Ubuntu 8.04 and tried the test commands for tkmedit and tksurfer as in "Testing your FreeSurfer installation. However, the graphics "flashed" when I typed the command and then disappeared. There was no error message on the terminal. The graphics showed up very briefly when I cricked on some places on the screen where the graphics flashed before. I also tried the centos4 32 bit version and the red hat 9 version, but ended up with the same problem. Is anyone having the similar problem? Thank you, Ryu Hashimoto

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postmortem data
by Mishkin Derakhshan 17 Dec '08

17 Dec '08

Hi, I have three questions regarding some postmortem data at high resolution (0.35 mm^3 isotropic). 1) A question was asked about the possibility of using postmortem scans in freesurfer back in sept 2007 and Bruce said: >Not easily, although we have some tools for doing this. They aren't packaged and distributed though. Any updates? 2) Is there a way to take advantage of this resolution and not resample to the 1mm^3 grid? 3) I only have one hemisphere. I am trying to flip the hemisphere to create a whole brain that can be used as input, but seeing as most of the pipeline splits things up into two hemispheres, is there a way to run Freesurfer with just one hemisphere from the start? thanks in advance as always, mishkin

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timecourse discrepancy question
by erickenb＠nmr.mgh.harvard.edu 17 Dec '08

17 Dec '08

We have been working on timecourse data that has had the prestim removed (at the mkcontrast-sess level). The timecourses obtained with roisummary-sess do not seem to correspond to the timecourses plotted with tksurfer. The discrepancy is two-fold: the peak latency and the overall timecourse shape. What could be the source of this discrepancy? This is particularly obvious for the ALC (alcohol) and PLAC (placebo) conditions - their peak activity is at the same timepoint in tksurfer but at different points in the text output (as shown in the Excel file) Included are: - The original text ouput file - Excel file with the text output along with the graph, - screen shots of the tksurfer timecourses and activity - on the left side is the timecourse of the activity with prestim removed and on the right is the timecourse with all the points We have also included some of the relevant script commands we used throughout the analysis. The entire working directory can be found here... /space/veles/3/users/sheeva/TEST-S51 This is the analysis I used... analysis.info analysis SNfir-test TR 2 designtype event-related nconditions 4 parname para.para fsd bold_SN funcstem fmcsm8 tpexclude -timewindow 18 -prestim 4 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 example of mkcont command...removing the prestim entire script can be found here.../space/veles/3/users/sheeva/TEST-S51/mkcont-sess.csh setenv aa 1 setenv cc 0 echo '0 0 0 1 1 1 1 1 1' | mkcontrast-sess -analysis SNfir-test -contrast CvFix-RMPS -a $aa -c $cc -rmprestim stxgrinder-sess -analysis SNfir-test -contrast CvFix-RMPS -sf 51-SN-intragp Finally, here is the csh that I used for making the timecourses.... setenv SUBJECTS_DIR /space/perun/3/users/cylix/Subjects foreach roi (lh-AC-med) foreach num (51) foreach ltr (a j) mri_label2label --srclabel /space/veles/3/users/sheeva/fMRIanal/fsavg-labels/RMPS/surface/LH/${roi}.label --srcsubject fsaverage --trgsubject sub${num}_recon --trglabel sub${num}_recon/label/${roi}.label --hemi lh --regmethod surface func2roi-sess -roidef ${roi}.label -labelfile /space/veles/3/users/sheeva/fMRIanal/fsavg-labels/RMPS/surface/LH/${roi}.label -d . -s sub${num}${ltr} -analysis SNfir-test roisummary-sess -analysis SNfir-test -roidef ${roi}.label -d . -sf SN51-a-j-RMPS -sumfile TEST-S51aj/Unmasked/LH/${roi}-unmasked.txt end end end Thank you Elizabeth

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GLUT: Fatal Error
by Catherine Hartley 17 Dec '08

17 Dec '08

Hi, My FreeSurfer installation was working fine several months ago, but recently when trying to launch tkmedit or tksurfer (from x11), I got: GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:0.0 GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:0.0 I tried installing the latest version. Same problem. I'm running Leopard 10.5.6 on a MacBookPro (Intel). Any ideas/suggestions would be welcome. Thanks, Cate Hartley

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tkregister2 error
by Susie Heo 17 Dec '08

17 Dec '08

Hello, When I try to use the Freesurfer command 'tkregister2' (or 'mri_convert', or any Freesurfer command for that matter) to read in my nifti files created using SPM, I receive the error message: "niiRead(): 2 dimensions in ../rsH794_1.nii; unsupported ERROR: could not read ../rsH794_1.nii as 24" Does anyone know what the problem is and how to fix it? Susie

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setting of fdr thresholds in qdec
by Michael Harms 16 Dec '08

16 Dec '08

Hello, I'm curious, what algorithm is used for setting the "mid" and "max" threshold values in QDEC when using the "Set Using FDR" button? And, what does the algorithm do for setting the "min" threshold when no single p-value is significant enough to satisfy the necessary inequality for the specified FDR Rate? In that case, is the resulting "min" just set to the -log10(p) of the most significant p-value? If easy to implement, it would be handy if the output to the terminal reported the number of vertices with P < than the FDR determined "min" threshold. 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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mris_wm_volume - different volume calculated over different FS versions
by Barkay, Gavriel 16 Dec '08

16 Dec '08

Hi, I used fs 4.0.1 to analyze my data, and accidentally, I happened to run mris_wm_volume on the same data, on another machine, which runs fs 4.0.5 The wm volume results were totally different between the two runs. mris_volume gives more similar, albeit not equal results on both machines. Is this a known issue? Does this happen with other morphometric utilities as well? Thanks, Gabi

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Freesurfer Installation on Ubuntu 6.06
by Hemalatha Sampath 16 Dec '08

16 Dec '08

Hi, I am trying to install freesurfer on Ubuntu 6.06 32 bit processor machine. I have downloaded the centos4-stable-pib-v4.1.0 and followed the installation instructions. I am installing it through remote login via ssh. During testing the installation by executing the tkmedit bert sample-001.mgz, the error message that is provided: GLUT: Fatal Error in tkmedit.bin: could not open display: When I do cat /etc/debian_version, I receive testing/unstable. Any help would be highly appreciated. Thanks, Hema

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