Freesurfer January 2008

freesurfer@nmr.mgh.harvard.edu

54 participants
69 discussions

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 that have not been done or are out of date.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

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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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which image is the best
by Feng-Xian Yan 25 Jan '08

25 Jan '08

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…. )

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vertex neighbourhood
by nima＠nmr.mgh.harvard.edu 24 Jan '08

24 Jan '08

hi surfers, Imagine that I need to know what are the closest N vertices (let's say n=100) to a given vertex (i mean two dimentionsal neighourhood on surfaces) . Any idea how to do that? anybody has a written code for this? cheers nima

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mri_cc segmentation fault
by Heath Pardoe 24 Jan '08

24 Jan '08

Hi, we've run into an issue running FS 4.01 on an Altix cluster (SuSE Itanium distribution - freesurfer-ia64-unknown-linux-gnu-stable4-20070918). On some subjects mri_cc falls over with a segmentation fault error (output pasted below). Running mri_cc -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz subject_id on the same subject on a different machine (Mac OS X) works ok. If we run mri_cc (on a subject that worked on the Altix) on our other machine we get identical output in recon-all.log. It seems strange that it works on some subjects and not on others. Any ideas as to what's going on? Please let me know if I need to provide any further information. Thanks Heath #-------------------------------------- #@# CC Seg Wed Jan 23 00:00:15 EST 2008 mri_cc -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz xxxx reading input aseg from aseg.auto.mgz writing aseg with cc labels to aseg.auto_CCseg.mgz reading aseg from xxxx/mri/aseg.auto.mgz reading norm from xxxx/mri/norm.mgz 43790 voxels in left wm, 72489 in right wm, xrange [117, 129] global minimum found at slice 123.0, rotations (-1.75, -2.25) final transformation (x=123.0, yr=-1.750, zr=-2.250): 0.999 0.039 -0.031 4.033; -0.039 0.999 0.001 4.772; 0.031 0.000 1.000 -3.697; 0.000 0.000 0.000 1.000; Segmentation fault (core dumped) Linux xxxx 2.6.16.53-0.16-default #1 SMP Tue Oct 2 16:57:49 UTC 2007 ia64 ia64 ia64 GNU/Linux recon-all exited with ERRORS at Wed Jan 23 00:05:46 EST 2008 -- Heath Pardoe, PhD Brain Research Institute Neurosciences Building Austin Health Banksia Street Heidelberg West, Victoria, 3081, Australia Phone: (+61 3) 9496 2576 Fax: (+61 3) 9496 4071 Email: h.pardoe(a)brain.org.au

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what is the prerequisite of cc in cortparc?
by walhovd＠nmr.mgh.harvard.edu 23 Jan '08

23 Jan '08

Hi I have a dataset originally processed with the Autumn 2005 FS version (2.2?). I know need wm segs, and in order to get this, I've tried to run -cortribbon -cortparc -cortparc2 -aparc2aseg -wmparc But the cc doesn't get labeled in the cortparc, and consequently (?) not in the wmparc either. I've also tried to rerun all of -autorecon3, but w/o difference. When rerunning recon-all -all, it gets fixed, but I would like to keep as much as possible as is, since I did lots of edits due to a temporal bias field problem. I've edited the asegs in some instances, and that is not kept by default. Grateful for tips on how far down in the processing stream I need to go to get correct wmparcs w/cc. Thanks, Kristine

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Freesurfer January 2008