Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Labelling Results on Tksurfer
by cthornto＠uci.edu 26 Jan '08

26 Jan '08

Hi I am using Freesurfer version 3.0.5 via Linux and I am trying to label my results on tksurfer. I have already loaded the group descriptor file and the overlay. I can visualize my results but when I click on these specific reasons, it does not tell me where these areas lie. How do I go about labellingmy results so that everytime I click on any one of these regions it will automatically tell me the name of the area? Any feedback is greatly appreciated. Christine Thornton

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recon-all error, COR-.info...
by Cameron Ellis 26 Jan '08

26 Jan '08

Hi, I keep getting an error when I submit jobs to seychelles that a COR-.info file cannot be found. Do you know why this would be? I pasted the full command and error log below. Thanks! Cameron recon-all -i /space/grouch/4/users/ponce/ponce_002d2/3danat/003 -i /space/grouch/4/users/ponce/ponce_002d2/3danat/004 -all -subjid Ponce_002d2 -force INFO: /autofs/space/grouch_004/users/ponce/Ponce_002d2 exists with -i, but -force specified. Deleting any previous source volumes INFO: SUBJECTS_DIR is /autofs/space/grouch_004/users/ponce Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0/stable4 -rw-rw-r-- 1 cameo zenuwgp 12297 Jan 26 10:00 /autofs/space/grouch_004/users/ponce/Ponce_002d2/scripts/recon-all.log Linux node0081 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux /autofs/space/grouch_004/users/ponce/Ponce_002d2 mri_convert /autofs/space/grouch_004/users/ponce/ponce_002d2/3danat/003 /autofs/space/grouch_004/users/ponce/Ponce_002d2/mri/orig/001.mgz mri_convert /autofs/space/grouch_004/users/ponce/ponce_002d2/3danat/003 /autofs/space/grouch_004/users/ponce/Ponce_002d2/mri/orig/001.mgz corRead(): can't open file /autofs/space/grouch_004/users/ponce/ponce_002d2/3danat/003/COR-.info $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from /autofs/space/grouch_004/users/ponce/ponce_002d2/3danat/003... Linux node0081 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sat Jan 26 10:14:40 EST 2008

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slice thickness
by Brian C. Schweinsburg, Ph.D. 26 Jan '08

26 Jan '08

I have an older dataset with .938 x .938 x 2mm resolution but good contrast and SNR. In previous posts, I have seen recommendations to not exceed 1.5 mm thickness for z-plane. I was wondering if this resolution was equally problematic for volume (aseg) labeling, similar to the surface path. Thanks, Brian

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Recon-all failing at CA Reg
by Caroline Chapman 25 Jan '08

25 Jan '08

Hello, I am having trouble with one subject during the recon-all process. It has failed twice at CA Reg: status file for recon-all Thu Nov 8 15:11:20 EST 2007 #@# MotionCor Thu Nov 8 15:11:20 EST 2007 #@# Nu Intensity Correction Thu Nov 8 15:18:50 EST 2007 #@# Talairach Thu Nov 8 15:21:26 EST 2007 #@# Intensity Normalization Thu Nov 8 15:23:01 EST 2007 #@# Skull Stripping Thu Nov 8 15:30:05 EST 2007 #@# EM Registration Thu Nov 8 15:33:05 EST 2007 #@# CA Normalize Thu Nov 8 15:42:54 EST 2007 #@# CA Reg Thu Nov 8 15:45:14 EST 2007 Linux node0052 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 athlon i386 GNU/Linux The brainmask, orig, and talairach look okay. Any ideas why this might be failing? Thanks! Caroline -- Caroline Chapman Research Technician Massachessetts General Hospital Geriatric Research, Education and Clinical Center VA Boston Healthcare System (857)364-2093 chapman(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] Accidentally stopped during recon-all
by Allison Stevens 25 Jan '08

25 Jan '08

Oops, I should have asked what version you were using. The -make flag is not in v3. Instead you can do: recon-all -hemi rh -autorecon3 -nosphere -s <subjid> This will run just the right hemisphere through the rest of -autorecon3. Doing -nosphere will skip the step before -surfreg which was already completed. Allison On Fri, 25 Jan 2008, Chris Watson wrote: > Hi Allison, this is the error message I received: > > [freesurfer@thalamus subjects]$ recon-all -make all -s <subjid> > ERROR: Flag -make unrecognized. > -make all -s <subjid> > > I'm running v3.0.4. > > Allison Stevens wrote: >> You can do: >> "recon-all -make all -s <subjid> and it will run all the remaining steps >> that have not been done or are out of date. >> >> >> >> On Fri, 25 Jan 2008, Chris Watson wrote: >> >>> Hello, >>> While running recon-all on a subject, my machine logged me off for an >>> unrelated reason. It was stopped during -autorecon3, specifically at >>> -surfreg (mris_register) for the right hemi. The left hemi was already >>> done, I believe. What would be the command to start from that step, and >>> continue to the end? >>> >>> Thanks, >>> Chris >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> > > >

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Accidentally stopped during recon-all
by Chris Watson 25 Jan '08

25 Jan '08

Hello, While running recon-all on a subject, my machine logged me off for an unrelated reason. It was stopped during -autorecon3, specifically at -surfreg (mris_register) for the right hemi. The left hemi was already done, I believe. What would be the command to start from that step, and continue to the end? Thanks, Chris

3 2

Installation/Setup Problems
by Cochrane Jamison 25 Jan '08

25 Jan '08

I have just installed the Mac OS X version 4.0.2 for PowerPC. Everything installed fine, but I have encountered errors beginning when I run the script file. When running the script, I get the following message: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /applications/freesurfer FSFAST_HOME /applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /applications/freesurfer/subjects MNI_DIR /applications/freesurfer/mni It then goes back to prompt. I was wondering why I was not receiving the following from the setup guide: GSL_DIR /usr/local/freesurfer/lib/gsl FSL_DIR /usr/local/freesurfer/fsl I then tried the next step from the guide even though I did not receive the last two lines above. When I tried to run tkmedit, from the freesurfer_home directory, on the bert orig.mgz file, I received this message: GLUT: Fatal Error in tkmedit.bin: could not open display: It then goes back to prompt. This is where I stopped and wrote this email. Any help would be great. Thank you in advance.

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Neuroimaging Research Position Available
by Jared Conley 25 Jan '08

25 Jan '08

Our neuroimaging lab at Brigham and Women's Hospital (Boston) is seeking a part-time (20 hrs/week) post-doc to come join our group and assist in human MRI analysis and post-processing. This individual will take a lead role in the analysis of structural and diffusion tensor MRI studies in an HIV cohort and a separate aging cohort. A candidate with FreeSurfer/FSL experience will have a distinct advantage (but is not requisite). If interested please respond with your CV attached. Thanks, Jared -- Jared Conley Department of Radiology/Neurology Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave, RF 394 Boston, 02115

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Talairach QA check failed
by Juergen Haenggi 25 Jan '08

25 Jan '08

Dear FS experts I tried to preprocess two T1-w. scans from a 7T scanner (dimensions 448x448x180; resolution 0.5x0.5x0.8mm) but the Talairch quality check failed. Fri Jan 25 08:47:06 CET 2008 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Fri Jan 25 08:47:07 CET 2008 /Applications/freesurfer/subjects/RO_reorient/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3873, pval=0.0643 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/RO_reorient/mri/transforms/talairach_avi.l og \n TalAviQA: 0.92008 z-score: -12 ERROR: Talairach QA check failed! z-score = -12 < -5 = threshold Darwin Macintosh-3.local 9.1.0 Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007; root:xnu-1228.0.2~1/RELEASE_I386 i386 recon-all exited with ERRORS at Fri Jan 25 08:47:07 CET 2008 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% Do you have any idea why that problem occurred? Does anyone have experience with scans acquired at 7T and FS? Another question is whether we can run FS with a resolution smaller that 1x1x1mm (larger matrix that 288x288x288)? Thanks in advance Best regards Juergen Haenggi ----------------------------------------------------------- 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) -----------------------------------------------------------

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Re: [Freesurfer] which image is the best
by Graham Wideman 25 Jan '08

25 Jan '08

Hi: Your description of the problem looks to me like there's some trouble with the interpretation of the 1404 mm dimension. It seems very unlikely that you have a scan that actually covers 1404 mm, so there must be a problem here. I would advise reading the header of the scan, which might require some program to read and interpret the header for you. Perhaps the header actually contains sensible information, such as: 1404 slices at 0.2 mmm --> ~ 280 mm field of view in that direction or 304 slices (or some other sensible number) instead of 1404. Anyhow, if you see this, it would suggest that the scan is OK, but FreeSurfer is having trouble loading it. A possible strategy in that case is to load the scan into some other software, resample to a grid closer to 1 mm grid, and trim/pad to make it 256 x 256 x 256. Software which might help there is AFNI. Also MRICro (Chris Rorden) might be useful, and even my GWRawMRIView for inspecting what your dealing with. http://grahamwideman.com/gw/brain/tools/gworc/index.htm Hope that helps, Graham At 1/25/2008 11:32 AM, you wrote: >Hi, > I have a problem about which image is the best to run. I had ran >the 1.5T data in freesurfer. Because the contrast of the 1.5T data was >too bad, I use the 3T data and rerun again. When I run, it says the >warning, > > >WARNING ============++++++++++++++++++++++++======================== >The physical sizes are (1404.00 mm, 256.00 mm, 256.00 mm), which >cannot fit in 256^3 mm^3 volume. >The resulting volume will have 1404 slices. >The freesurfer tools should be able to handle more than 256 slices. >If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) >=====================++++++++++++++++++++++++=============== > > >This problem confused me. What can I do? Could you tell me what image >is freesurfer I can run and get the best results? (about dimension¡K. ) > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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