Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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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Newbie question - read error, segmentation faults and errors loading volumes-oh my
by Sheyna Gifford 17 Jul '07

17 Jul '07

Dear Freesurfer List, I have used mri_convert as per the tutorial, to great the following mgz files from dicoms: 001/mri/orig/001.mgz and 002/mri/orig/002.mgz They were created with the following call or the appropriate varient: $mri_convert -it dicom -ot mgz 002/mri/orig/002/ 002.mgz There were no major errors that appeared during the conversion, and the files that were created are valid reconstructions. I have opened them both in Neurolens and they look exactly as they should. However, when I try to tkmedit them, I get the following error: $ tkmedit 001 001.mgz mghRead(/Applications/freesurfer/subjects/001/mri/001.mgz, -1): read error Error: Loading volume 001/mri/orig/001.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. A friend suggested that I use the COR format instead of going through the mgz intermediate, which I did with the commands: $ mri_convert 002/mri/orig/002/IM-0001-0010.dcm 002 -ot cor However, I get the same error. These subjects-001 and 002-are in the default freesurfer/subjects folder. Tkmedit itself works, as I was able to run through the entire tutorial without a hitch. These are T1-weighted structural images that I am just trying to take a look at, in my first FreeSurfer foray. Not trying anything fancy, I don't think. Any help, guidance and/or suggestions would be appreciated. Sincerely, sgifford -- Sheyna Gifford Research Specialist Magnetic Resonance Imaging Research Facility Brown University Box G-L 401-863-6513

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freesurfer in cygwin
by 申林 17 Jul '07

17 Jul '07

hi, I have downloaded freesurfer in WINDOWSXP and want to run it via Cygwin. But it don't work. Is there possibility to run it ? The freesurfer I used is the public copy. I follow the "LinuxInstall" and type : tar xzvf freesurfer-Linux-rh9-stable-pub-v3.0.5-full.tar.gz export FREESURFER_HOME=<j:/cygwin/usr/local/>/freesurfer export SUBJECTS_DIR=<=<j:/>/freesurfer . ${FREESURFER_HOME}/SetUpFreeSurfer.sh and then, any command seems don't work, (e.g. mri_convert , tkmedit, tksurfer) and reture erro like this (bash: mri_convert: command not found). how to resolve the problem and how to run it normally in WINDOWSXP? thank you! Shen Lin -- Lin Shen, MMS, Department of Neurology, The First Affiliated Hospital, ChongQing Medical University No.1, Yixueyuan Road, ChongQing, 400016 China Phone: +86 23 13193076520 E-mail: shenlin918(a)gmail.com

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