Freesurfer

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30076 discussions

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

2 1

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

2 1

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

2 1

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

2 1

?h.volume vertex-wise
by Juergen Haenggi 30 Aug '07

30 Aug '07

Dear Freesurfer users We would like to analyze cortical volumes vertex-wise. We recognized that ?h.volume are not produced by the recon-all command. I have read the questions posted some days ago by Rafael Huber concerning the same problem. One proposed solution was to multiply ?h.area times ?h.thickness at each vertices. To do this read_curv.m and the write_curv.m functions in MATLAB were suggested. We tried it but failed maybe due to our insufficient knowledge in MATLAB programming. The first step (read_curv.m) works and produced a vector of curvature (small negative values) instead a vector of thickness (positive values between 1.5 and 3.5 mm) as we expected. What happens here? The command write_curv.m does not work at all. Is there any short documentation about multiplying images in MATLAB? We appreciate any suggestions about that issue. Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

xform avesurf-> subject
by Kirk, Gregory 29 Aug '07

29 Aug '07

Hi All, I want to click on a point on my average surface for my group and ' save point' load a T1 or orig subject in the group with tkmedit and 'goto saved point' i.e. map by the inverse of the transform that embeded the subject surface into the average surface and see the point on the structural that mapped to it. Seems I remember this can be done, I have to load a transform I think. looked through the docs and mail archive but perhaps I was not thinking of the best key to search the archive. thankx Greg.

2 1

resampling thickness
by Goldman, Aaron (NIH/NIMH) [C] 29 Aug '07

29 Aug '07

Hi, for a group of subjects, I was interested in getting ascii files for each subjects' thickness, resampled to an average subject. I know how to do the resampling using something like: mris_preproc --fsgd fsgd.txt --target average --hemi lh --meas thickness --out file.mgh but was wondering what I'd need to do to get individual files that can be read by a text editor, rather than the one big mgh file. Is there some kind of flag or subsequent command I can add to do that? Thanks, -Aaron-

2 1

ReconAllDevTable Q.
by Jamie Hanson 28 Aug '07

28 Aug '07

Which version of Freesurfer is the ReconAllDevTable on the wiki for? Is it for v.3.0x or v.4.0? ... has anything changed in that regard for v.4.0? jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 Phone: (608) 262-5148 ***Please note my new email: jamielarshanson(a)gmail.com***

2 1

Standard deviation map
by Inês Souta 28 Aug '07

28 Aug '07

Hello, After computing the average thickness of an average subject (prior to Qdec), how can I estimate and get a map of standard deviations of the thickness measures across the subjects I've averaged. Thanks, Ines

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