Freesurfer May 2009

freesurfer@nmr.mgh.harvard.edu

81 participants
126 discussions

average 4d volume
by jake＠nmr.mgh.harvard.edu 11 May '09

11 May '09

Hi! I tried to use mri_xvolavg to average a 4d nii volume, but does it need me to list each 3d volume separately? Is there a command that I can use to produce an average of a 4d volume, in one 3d image? Thanks in advance!! Jake

2 1

Unable to Open GUI
by Andrew Jahn 11 May '09

11 May '09

Hi, We are operating x86_64 redhat linux on a server, and we recently installed FreeSurfer on the surfer to help with running multiple recon-all's. However, whenever I attempt to run tkmedit or tksurfer, I get the following error: [andrew@scan2 Anatomicals]$ tkmedit Focus_reg_009 brainmask.mgz GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not surrported by display: :1.0 Is this a problem specific to the VNC Viewer I am using (Chicken of the VNC on a Mac OS X), or some other compilation problem? Thanks! -Andrew

1 0

tkmedit multiple orientation view
by Krajcsi Attila 11 May '09

11 May '09

Hi All, Is it possible to start tkmedit with the multiple orientation view as default? Thank you, Attila

2 4

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

2 1

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

2 1

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

2 2

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/

1 0

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

3 3

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

1 0

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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Freesurfer May 2009