Freesurfer July 2007

freesurfer@nmr.mgh.harvard.edu

61 participants
99 discussions

recon-all Is-Running
by Doug Greve 19 Jul '07

19 Jul '07

I've just added a new feature to the dev version of recon-all to help you manage your processes. When you launch recon-all, it will create a file called IsRunning.lh+rh in your subject/scripts folder. When recon-all finishes (with or without errors), this file will be deleted. So, the presence of this file indicates that recon-all is being run on this subject. This file may also exist if recon-all died in a way that it could not clean up (eg, control-C). The contents of the file indicate information about the process that will allow you to determine whether it is still running or not: date Thu Jul 19 19:24:30 EDT 2007 processid 10196 hemi lh rh host icebox user greve Linux icebox 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux You can then ssh to the host and use the unix 'ps' command to check for the existence of the process. If you run recon-all on this subject again while this file exists, it will exit indicating that the subject is already being processed or recon-all died uncleanly. If you want it to run regardless, then add -no-isrunning to the command-line. It will not delete the IsRunning file, just ignore it. When you run the hemispheres separately (ie, -hemi lh or -hemi rh), it will create a IsRunning.lh or IsRunning.rh file. This allows you to run recon-all for both hemis in parallel. If this file exists or IsRunning.lh+rh exists, then again recon-all will exit telling you that the subject is already being processed or recon-all died uncleanly. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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gca file format
by lan lin 19 Jul '07

19 Jul '07

I got some question about gca file format. What does totaltraining means? GIBBS_NEIGHBORS is more 6 neighboring voxels. What is relationship between them? From 1:6 , which one is left, right etc? thanks

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opening aseg.stats file
by Lindsay Casmaer 19 Jul '07

19 Jul '07

Hello all, I am finally gearing up to look at the stats generated from processing. Though when I open the stats file as a tab/space delimited in excel, it really looks messy. Any other programs that would be good to view the tables with? Thanks. -Lindsay

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one list thing
by Bruce Fischl 19 Jul '07

19 Jul '07

if you could include the funding source (particularly NIH institutes!) that would be great.

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mri_glmfit
by Lars M. Rimol 19 Jul '07

19 Jul '07

Hi, Please ignore my previous mail, I did not see that "external" on the y axis means dependent variable (blame it on the early morning blues...) -- yours, LMR

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clarification
by Bruce Fischl 19 Jul '07

19 Jul '07

Two more thing: please include the # of subjects that you have analyzed, and any clinically relevant study that uses FreeSurfer can be included (included DTI and fMRI). thanks again, Bruce

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mri_glmfit
by Lars M. Rimol 19 Jul '07

19 Jul '07

Hi, I ran mri_glmfit with a fsgdf looking (in principle) like this: GroupDescriptorFile 1 Title MyTitle Class Group1 plus blue Class Group2 circle green Variables ICV Input subjid1 Group1 10000 Input subjid2 Group2 20000 Dependent variable iscortical thickness. When I "load group descriptor file", i.e. y.fsgd, and click on a vertex and choose "View by class", the button to the right of that has only one level: "ICV", and the x axis of the graph also has the title ICV (and units that seem to represent ICV). However, I am interested in visualising the dependent varable cortical thickness per vertex, not the continuous predictor/regressor ICV. Have I made a mistake in the fsgdf? Thank you! -- yours, LMR

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clinically relevant morphometry
by Bruce Fischl 19 Jul '07

19 Jul '07

Hi All, we've been asked by NCRR to quantify our impact in clinical conditions. If all of you using FreeSurfer to study something relevant to human health (e.g. aging, AD, etc...) could send me a brief email containing: name and PI of the study subject processed to date 1 sentence describing the study I would really appreciate it. thanks, Bruce -------------------------------------------------------- Bruce Fischl email: fischl(a)nmr.mgh.harvard.edu Mass. General Hosp. NMR Center. tel:(617)-726-4897 Rm. 2301, Building 149, 13th Street fax:(617)-726-7422 Charlestown, MA 02129 USA

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Segmentation
by Gallo, Antonio (NIH/NINDS) [F] 19 Jul '07

19 Jul '07

Hi All, Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded segmented maps. Precisely - as an example - in the attached figure you can see that in the case of left insula WM, part of the tissue was classified as GM (in brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the tissue is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern. I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential errors in the generated values of thickness and volumes as well? If so, is there any way I can correct for this? Thank you in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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error while loading shared libraries
by Andrew Ellison 18 Jul '07

18 Jul '07

Hi My Name is Andy Ellison and im Using (attempting) Freesurfer at Boston University. Upon my first attempt to install freesurfer on Centos 5 (i understand that the release was specific for Centos4 but unsure if it would have an affect) i received this error message /usr/local/freesurfer/bin/tkmedit.bin: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory I read online another person had this problem so I commented out a small line of code in the FreeSurferEnv.csh source ${FSL_DIR}/etc/fslconf/fsl.csh This had no effect so I am emailing you in hopes you know what i can do. This is the second time i had this issue, I had earlier thought it was a problem with my installation of FSL, but upon a total uninstall of centos5 and reinstall it still is uncooperative, any help would be really appreciated, thanks Andy

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Freesurfer July 2007