Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

why no answer?
by Joongnam Yang 16 Oct '06

16 Oct '06

I posted the following question again, since I didn't get any response. I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following, mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --out AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint and got the following error message, MRISreadCurvature: could not open /home/nam/AVERAGE/average/surf/lh.thickness No such file or directory In the surf directory, I DID find "lh.avg_thickness". Would someone please let me know how to remedy this? Nam.

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Re: [Freesurfer] Intensity/Conversion problem
by Derin Cobia 13 Oct '06

13 Oct '06

Bruce, I've been getting values from around 188-255 in the wm. -Derin

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mri_convert on 64bit vs 32bit
by Niels Bergsland 12 Oct '06

12 Oct '06

Hi, I am experiencing quite a strange problem. I have a set of DICOMs that when I run the following on a 32bit machine, it works fine: mri_convert 031G0110.101.dcm 001.mgz When I run the exact same command (from within the same directory) on the 64 bit machine, I get the following error: "Currently non-Siemens mosaic image cannot be handled. Exit" (I should note that these are not actually mosaic images, they are individual) mri_convert --all-info on the 32 bit machine yields the following: mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/12-20:37:40-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: niels Machine: freya.bnac Platform: Linux PlatformVersion: 2.6.9-42.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 and on the 64 bit machine: mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/10/12-20:38:29-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: niels Machine: giza Platform: Linux PlatformVersion: 2.6.9-22.ELsmp CompilerName: GCC CompilerVersion: 30400 We have used the 64 bit install extensively before and never run into this issue. Any insight? Thanks! Regards, Niels Bergsland

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mri_extract_label
by Behrang Nosrat Makouei 12 Oct '06

12 Oct '06

Hi everyone, My goal is to have the cortical segmentation in subject's native space in analyze format volume images. the series of commands i run are: mri_extract_label aparc+aseg.mgz LABELNUM outVolume.mgz mri_convert -rt nearest -rl rawavg.mgz outVolume.mgz outLabelSegmentation.img the problems I have are: 1- the segmentations I get are noisy 2- the segmentations are not as good as they look like in Surface segmentations and I can clearly see some holes and discontinuities at my final volumes. any suggestions? best, -- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016

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func2roi-sess error?
by Lei.Zhang＠uniklinik-freiburg.de 12 Oct '06

12 Oct '06

Hi All, I tried func2roi-sess with my data, it ran quickly and gave one message at the end 'Unknow user: greve', but no other errer reports. I checked the sessid directory and found it created the -roisef directory, but no files in it. I think there must be something wrong, associated with user? Any hints would be appreciated! Thanks, Lei

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mri_vol2surf error
by Joongnam Yang 12 Oct '06

12 Oct '06

Dear all, I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following, mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --out AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint and got the following error message, MRISreadCurvature: could not open /home/nam/AVERAGE/average/surf/lh.thickness No such file or directory In the surf directory, I DID find "lh.avg_thickness". Is this an error of Freesurfer? Would someone please let me know how to remedy this? Nam.

1 0

dilating/eroding wm volume
by Bo Shi 12 Oct '06

12 Oct '06

Good morning! I have a dataset whose white matter volume is a bit too aggressive and I'd like to erode it a bit - is there a quick way to do this using tkmedit or one of the command line tools? Thanks, Bo

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wm and subcortical gray matter volumes
by Bo Shi 12 Oct '06

12 Oct '06

I didn't want to clutter up one thread with two unrelated questions; Is there a quick way to get a total count for wm/gm volume and subcortical gray matter? AFAIK, the output is divided into a much finer structures... Thanks!

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Intensity/Conversion problem
by Derin Cobia 12 Oct '06

12 Oct '06

I seem to be having some difficulty in converting my flash images into FS format for processing. After using mri_convert my orig.mgz files become excessively bright compared to the original analyze file, thus creating poor autorecon1 output, etc. See the attached jpgs of before and after shots. Also, here's the command I'm using: mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz *subjectid*.img mri/orig/001.mgz Am I doing something wrong? Thanks. -Derin

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setenv FREESURFER_HOME /usr/local/freesurfer
by Juergen Haenggi 10 Oct '06

10 Oct '06

Dear Freesurfer users I am starting to work with Freesurfer, but I have no experience with Unix. For the installation example in the documentation, there is the command: setenv FREESURFER_HOME /usr/local/freesurfer but this command (setenv) could not be found. What happens? What is FREESURFER_HOME? A directory, a file or something else? Thanks for help in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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