Freesurfer September 2007

freesurfer@nmr.mgh.harvard.edu

69 participants
99 discussions

Subgenual problems
by Alex Fornito 05 Sep '07

05 Sep '07

Hi all, I've been having problems getting accurate surfaces in the subgenual cingulate region, as illustrated in the attached pics. I previously posted to the list about this, and you sent me a newer mris_surf for an older version of freesurfer that fixed the problem in some, but not all cases. It seems like the new version (included with 4.0) is still giving me some grief. Any suggestions re: what I can do? Thanks for your help, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia Phone: +61 3 8344 1861 Fax: +61 3 9348 0469 Email: fornitoa(a)unimelb.edu.au www.psychiatry.unimelb.edu.au/mnc

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unpacksdcmdir error
by Akram Bakkour 04 Sep '07

04 Sep '07

when I unpack a single run I get an error which I've never encountered before. I get the same error in std and dev cd /space/madrc/1/users/MADRC_ARCHIVE/MGH_MADRC_ARCHIVE/MGH_MADRC_ARCHIVE_BAY4 unpacksdcmdir -src 08242007_4TT_clindem93/dicom -targ 08242007_4TT_clindem93/raw -run 15 MEMPRAGE mgz MEMPRAGE.mgz here is the end of the output Run 15 ----------------------------------------- Tue Sep 4 11:52:48 EDT 2007 15 MEMPRAGE mgz MEMPRAGE.mgz mri_convert 08242007_4TT_clindem93/dicom/00140001 08242007_4TT_clindem93/raw/MEMPRAGE/015/MEMPRAGE.mgz --sdcmlist 08242007_4TT_clindem93/raw/MEMPRAGE/015/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation when I run mri_convert 08242007_4TT_clindem93/dicom/00140001 08242007_4TT_clindem93/raw/MEMPRAGE/015/MEMPRAGE.mgz --sdcmlist 08242007_4TT_clindem93/raw/MEMPRAGE/015/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom I get this ERROR: cannot extract sDiffusion.alBValue[1] from 08242007_4TT_clindem93/dicom/00140001 Segmentation fault Any suggestions? Thanks! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

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mri convert
by eozdemir＠nmr.mgh.harvard.edu 04 Sep '07

04 Sep '07

When I try to convert dicoms to spm format, I get the following error which I have not encountered before. I get the same error for both anatomical dicoms and functionals. "ERROR: cannot extract sDiffusion.alBValue[1] from anat/374000-2-1.dcm Segmentation fault" Does anybody know how I can fix this? Thanks Elif

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a white matter mask that excludes sub-cortical structures
by bell0368＠umn.edu 04 Sep '07

04 Sep '07

Hello, I am trying to create a white matter mask that excludes sub-cortical structures for use in calculating FA from a dti scan. I am still using version 3.0.5 for now. I was considering combining the surface white matter mask and the aseg mask of the sub-cortical structures, but was not sure if this was valid. I am concerned because the surfaces are calculated separetly from the aseg and there will likely be some areas of disagreement between the two, for example in the hippocampus. Any suggestions would be appreciated. Does the new version 4.0.0 dti package include any helpful tools? Chris Bell University of Minnesota

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ERROR: mri_convert --child killed: segmentation violation
by Pratap Kunwar 04 Sep '07

04 Sep '07

Hi, I got the following error when i tried to unpack the MRI data. It used to work perfectly fine in my Linux computer but i encounterd this problem while i tried to unpack new MRI data today. I also tried for another old data but still got same error "child killed: segmentation violation". i will appreaciate for help Pratap Kunwar unpacking config ------------------ {1 scout DICOM blah} {3 3danat COR blah} {4 3danat COR blah} {5 fm_dti DICOM blah} {6 fm_dti DICOM blah} {7 dti DICOM blah} {14 t2conv bshort f} {15 t1epi bshort f} {16 fm_epi DICOM blah} {17 fm_epi DICOM blah} {18 bold bshort f} {19 bold bshort f} {20 bold bshort f} ----------------------------------- --------------------------------------------------------- Run 1 ----------------------------------------- Tue Sep 4 11:09:26 EDT 2007 1 scout DICOM blah --------------------------------------------------------- Run 3 ----------------------------------------- Tue Sep 4 11:09:27 EDT 2007 3 3danat COR blah mri_convert /space/archive/134/siemens/TrioTim-35006-20070826-122449-774000/774000-3-1.dcm /space/galen/2/users/carl/HR_LR18VvI/test_sept4/3danat/003 --sdcmlist /space/galen/2/users/carl/HR_LR18VvI/test_sept4/3danat/003/flf -ot cor --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.0-20070901 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_002/users/carl/HR_LR18_recon/ PWD: /space/galen/2/users/carl/HR_LR18VvI/test_sept4 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name--rfa1335 2) the entire command-line executed unpacksdcmdir -src /space/archive/134/siemens/TrioTim-35006-20070826-122449-774000 -targ /space/galen/2/users/carl/HR_LR18VvI/test_sept4 -fsfast -cfg /space/galen/2/users/carl/HR_LR18VvI/test_sept4/cfg.file -unpackerr 3) the error message generated

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New Freesurfer v4.0.0
by Nick Schmansky 04 Sep '07

04 Sep '07

A new version of Freesurfer is now available for download from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download The list of new features, bug fixes, and known issues is found on the ReleaseNotes page: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Users are reminded that in general, subjects should be processed by a single version of Freesurfer (ie. in a group study, subjects should not have been processed by different versions of Freesurfer). Older versions of Freesurfer are available upon request. The Freesurfer Team.

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Re: Re: [Freesurfer] Average Volume
by Rafael Huber 04 Sep '07

04 Sep '07

Our goal is to get a file of average volume. As i understand the make average command it takes the whole information of e.g. ?h.thickness out of every /surf folder of every subject and creates an average ?h.thickness file and saves it to /average/surf. i try to do the same with the ?h.volume.mgz files, which we created with the matlab command you proposed us. we made it as far that we have two ?h.volume.mgz files in each subjects surf folder and we would like to continue the group analyses process. Hi Rafael, sorry, I don't understand. What do you mean " Problems appeared later on, because we didn't find a difference in the average folder compared to using the command without lh.volume.mgz files in the surf folder." What problems? What kind of differences are you looking for and how? Bruce On Mon, 3 Sep 2007, Rafael Huber wrote: Dear freesurfer users Do you have an idea how to create an average ?h.volume file? Our goal is to create a file with average volumes for our subjects, to follow the group analysis. We know that the idea of using a volume measure isn't implemented in the freesurfer software. We runned the make_average_subject command in hope to find something like an ?h.volume file in the average folder as there are files for the other measures like thickness, area, curvature. Before we runned the make_average command we followed the advice of Bruce Fischl to create .mgh files in matlab with the following command: [thickness, f] = read_curv('lh.thickness') ; [area, f] = read_curv('lh.area') ; volume = thickness .* area; save_mgh(volume, 'lh.volume.mgz', eye(4)); This functioned very well and we got our lh.volume.mgz files in the surf folder. Problems appeared later on, because we didn't find a difference in the average folder compared to using the command without lh.volume.mgz files in the surf folder. We're now not sure if we should continue like normal, or what exactly to do. Has somebody an idea. Best regards Rafael Huber _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Average Volume
by Rafael Huber 03 Sep '07

03 Sep '07

Dear freesurfer users Do you have an idea how to create an average ?h.volume file? Our goal is to create a file with average volumes for our subjects, to follow the group analysis. We know that the idea of using a volume measure isn't implemented in the freesurfer software. We runned the make_average_subject command in hope to find something like an ?h.volume file in the average folder as there are files for the other measures like thickness, area, curvature. Before we runned the make_average command we followed the advice of Bruce Fischl to create .mgh files in matlab with the following command: [thickness, f] = read_curv('lh.thickness') ; [area, f] = read_curv('lh.area') ; volume = thickness .* area; save_mgh(volume, 'lh.volume.mgz', eye(4)); This functioned very well and we got our lh.volume.mgz files in the surf folder. Problems appeared later on, because we didn't find a difference in the average folder compared to using the command without lh.volume.mgz files in the surf folder. We're now not sure if we should continue like normal, or what exactly to do. Has somebody an idea. Best regards Rafael Huber

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Doubts regarding maximum thickness
by Pedro Paulo Oliveira Jr 03 Sep '07

03 Sep '07

We are conducting a study and so far have analyzed 40 subjects using FreeSurfer. We have some doubts regarding cortical thickness: 1) Why the maximum value of cortical thickness in lh.thickness or rh.thickness is 5.0 mm? We have case in which clearly the thickness is greater than that in some areas. 2) In the thickness scale for one individual there are colors for negative values. We don't see a topological or mathematical sense in negative thickness, is there any info on that? 3) We found out that in many cases even in healthy subjects the Insular cortex area presents 5.0 mm thickness in a great area. We think the algorithm may face difficulties in this area since its much convoluted. Is that assumption true? Thanks in advance for the help. Pedro Paulo Oliveira Jr InRad - HCFMUSP

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Freesurfer September 2007