Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Error with skullstripping
by Ed Gronenschild 08 May '09

08 May '09

Hi, During processing with the command recon-all autorecon-all -s mysubject I got an error with the following message: mri_watershed error: GLOBAL region of the brain empty ! What to do? Can I use a different option for the watershed algoritme? Ed

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localGI not recognised
by Prapti Gautam 08 May '09

08 May '09

Dear all, I am trying to measure local Gyrification Index in my subjects and can't get started. I get the following error: Flag -localGI not recognised I have Matlab and its Image processing toolbox installed in my computer and am running freesurfer version 4.0.2. Do I have to have the newer version of freesurfer installed to use lGI? Thanks, Prapti

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Unexpected Long processing time
by Wayne Su 07 May '09

07 May '09

I re-ran over 400 scans by using Freesurfer 4.3.0 on Mac OS 10.5.6. Well, I¹m very happy on the results. Anyway there are two issues I encountered: 1) I have 3 scans hanging on the last second step when creating the aparc+aseg.mgz by using mri_aparc2aseg (more precisely is the ³labeling slice² processing) for over one week though it finally finished. The log is attached. 2) I have some scans reported ³mris_fix_topology failed! (euler number != 2)² so recon-all exited with errors. I didn¹t find there was any problem when I used the V4.0.5. I attached the log as ³recon-all2.log². Thanks. Wayne

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mri_cc / aseg issue.
by Jamie Hanson 07 May '09

07 May '09

Hi Freesurfer folks- I created a custom aseg atlas and now, I am running into some issues w/ recon-all. Here is part of my terminal output... --- cp aseg.auto.mgz aseg.mgz #-------------------------------------- #@# CC Seg Wed May 6 20:40:19 CDT 2009 mri_cc -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz 162_aseg reading input aseg from aseg.auto.mgz writing aseg with cc labels to aseg.auto_CCseg.mgz mri_cc: volume /study/eemri/data/proc/freesurfer/162_aseg/mri/aseg.auto.mgz already has CC in it reading aseg from /study/eemri/data/proc/freesurfer/162_aseg/mri/aseg.auto.mgz Linux pasilla.keck.waisman.wisc.edu 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 07:03:59 EDT 2009 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed May 6 20:40:22 CDT 2009 ------ Thoughts? Did my aseg creation go awry? Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

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Help with skull strip
by Drosos, Athena 07 May '09

07 May '09

Hi, I am part of a group interested in measuring cortical thickness and we have had problems with skull stripping. We read on the mailing list that you are not supposed to delete the skull with the edit voxel tool on the brainmask.mgz because it affects the surfaces. What would be an appropriate way to delete/remove the skull? We tried lowering the watershed threshold (normally at 5) to 3, and found skull still being classified as brain as well as some brain missing. Thank you, I look forward to hearing your response. Sincerely, Athena

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ERROR: could not read header info from T1 or orig
by anita di iasio 07 May '09

07 May '09

Hi, I have a problem: In the past Freesurfer runs and all go right. Now when I run tksurfer command, a error message appears: surfer: current subjects dir: models/buckner_data/tutorial_ subjs/group_analysis_tutorial/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/anita/models/buckner_data/tutorial_subjs/group_analysis_tutorial ERROR: could not read header info from T1 or orig in models/buckner_data/tutorial_subjs/group_analysis_tutorial//004/mri It is strange because the error message appears with tutorial data. Can anybody help me? Thanks, Anita

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Re: [Freesurfer] Problem with space in directory or file name
by Ed Gronenschild 07 May '09

07 May '09

Hi Sita, That doesn't work. I have to write a script to remove the space. ed On 7 May 2009, at 1:15, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Hi Ed, > > You can try inserting a backslash and then a space in the filename. > eg.. if you have 'dicom file.dcm', you might want > to try > > recon-all -all -i dicom\ file.dcm -s ............. > > > Sita. > > > > > On Wed, 6 May 2009, Ed Gronenschild wrote: > >> Hi, >> >> Whenever I want to convert DICOM files to .mgz file I have to >> remove spaces in the directory name or file names otherwise >> recon-all -i ... -s ... will not work. >> Bracketing the names within quotes will not help. >> Is there some workaround? >> >> ed >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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Problem with space in directory or file name
by Ed Gronenschild 06 May '09

06 May '09

Hi, Whenever I want to convert DICOM files to .mgz file I have to remove spaces in the directory name or file names otherwise recon-all -i ... -s ... will not work. Bracketing the names within quotes will not help. Is there some workaround? ed

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problem downloading freesurfer
by Dana W. Moore 05 May '09

05 May '09

I am trying to download FreeSurfer onto a different Linux machine. I am able to download, but when I try to unzip the files, I get this error message: gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now I have tried downloading it repeatedly with the same outcome. Do you know what the problem might be? I am downloading the <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.3.0/freesurfer-Linux…>freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz file. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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fMRI FOV issue (Bay 8)
by Dave Brohawn 05 May '09

05 May '09

Hello, My bugr info is at the bottom, if needed: I was doing a recon-all on one of our subjects, and I received this error message: **************************************** ERROR! FOV=320.000 > 256 Include the flag -cw256 with recon-all! **************************************** I pasted this error message into the archives, and saw Nick had asked someone with a similar problem to check the FOV of their subject to see if it was greater than 256 via mri_info orig.mgz. Our subject, FB0011055B, has an FOV of 320, and dimensions 320 X 320 X 320. This is unusual because we opened the same set protocol as we usually do and did not make any adjustments to the FOV or slice parameters. Most of our subject's orig.mgz info looks like this - Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2200.00 msec, TE: 1.54 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.7146 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 24.6542 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -26.7758 talairach xfm : /autofs/space/seymour_001/users/folate_subjects/FB0011053B/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 127.2854 0.0000 0.0000 1.0000 -103.3458 0.0000 -1.0000 0.0000 101.2242 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 127.2854 -0.0000 -0.0000 -1.0000 101.2242 -0.0000 1.0000 -0.0000 103.3458 0.0000 0.0000 0.0000 1.0000 This subject's is different, and it looks like this: Volume information for orig.mgz type: MGH dimensions: 320 x 320 x 320 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 320.000 dof: 0 xstart: -160.0, xend: 160.0 ystart: -160.0, yend: 160.0 zstart: -160.0, zend: 160.0 TR: 2200.00 msec, TE: 1.54 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.2500 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 158.7500 0.0000 0.0000 1.0000 -160.0000 0.0000 -1.0000 0.0000 160.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 158.7500 -0.0000 -0.0000 -1.0000 160.0000 -0.0000 1.0000 -0.0000 160.0000 0.0000 0.0000 0.0000 1.0000 Any ideas as to why this would happen? Also, what does this -cw256 flag do and will it fix the issue? **************************************** ERROR! FOV=320.000 > 256 Include the flag -cw256 with recon-all! **************************************** Thank you, Dave Brohawn FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090503 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects PWD: /space/seymour/1/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects cd /space/seymour/1/users/folate_subjects

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