Freesurfer October 2005

freesurfer@nmr.mgh.harvard.edu

49 participants
62 discussions

Re: [Freesurfer] Error:
by Michele Grubb 06 Oct '05

06 Oct '05

Thank you Nick! Michele >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 10/5/2005 12:12:44 PM >>> Michele, >From looking at the recon-all.log, it appears that you have an older version of freesurfer than contained a bug whereby mris_anatomical_stat was missing the -mgz flag. You could either: 1) manually run mris_anatomical_stats as shown: cd /home/amc/AMCSubjects/18014B mris_anatomical_stats -mgz -f scripts/rh.aparc.stats -b -a \ label/rh.aparc.annot 18014B rh or 2) install a new 'dev' release of freesurfer and rerun your subject: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Nick On Wed, 2005-10-05 at 11:33 -0400, Michele Grubb wrote: > Ok-here is the file. > > Michele > > >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 10/4/2005 1:49:48 PM >>> > Hi Michele, > > you need to send us more info than this. Preferably the whole > recon-all.log file. > > Bruce > On Tue, 4 Oct 2005, Michele Grubb wrote: > > > Dear FS Help: > > > > When running recon-all -subjid 18014B -autorecon3 -mgz > > > > we got the following error message: > > > > autorecon3 exited with errors- > > ERROR: mris_anatomical_status exited with nonzero status > > > > What does this error mean? What can we do to reconcile this? > > > > Thank you. > > > > Michele > > > > > --------------------------------------------------------------------------------------------------- > > Michele C. Grubb, PhD > > Research Development > > Neurosciences Advanced Imaging Research Center > > 47 New Scotland Ave., MC65 > > Albany, NY 12208 > > > > office: (518) 262-0810 > > fax: (518) 262-0802 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Error:
by Michele Grubb 05 Oct '05

05 Oct '05

Ok-here is the file. Michele >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 10/4/2005 1:49:48 PM >>> Hi Michele, you need to send us more info than this. Preferably the whole recon-all.log file. Bruce On Tue, 4 Oct 2005, Michele Grubb wrote: > Dear FS Help: > > When running recon-all -subjid 18014B -autorecon3 -mgz > > we got the following error message: > > autorecon3 exited with errors- > ERROR: mris_anatomical_status exited with nonzero status > > What does this error mean? What can we do to reconcile this? > > Thank you. > > Michele > > --------------------------------------------------------------------------------------------------- > Michele C. Grubb, PhD > Research Development > Neurosciences Advanced Imaging Research Center > 47 New Scotland Ave., MC65 > Albany, NY 12208 > > office: (518) 262-0810 > fax: (518) 262-0802 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Keeping edits
by Fornito, Alexander 04 Oct '05

04 Oct '05

HI, I've been running autorecon2-wm or -cp after making edits to the brain volume as well, but it seems that the brain edits are not retaned in the final output. Is there a flag I'm missing? Also, to confim, If I run autorecon2-cp with the -keepwmedits flag, this will retain any edits made to the wm volume won't it? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito(a)wh.org.au

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Brain mask
by Satrajit Ghosh 04 Oct '05

04 Oct '05

Is there an easy way to generate a brain mask like aseg.mgz but with the cortical parcellation included? Thanks, Satra

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Error:
by Michele Grubb 04 Oct '05

04 Oct '05

Dear FS Help: When running recon-all -subjid 18014B -autorecon3 -mgz we got the following error message: autorecon3 exited with errors- ERROR: mris_anatomical_status exited with nonzero status What does this error mean? What can we do to reconcile this? Thank you. Michele --------------------------------------------------------------------------------------------------- Michele C. Grubb, PhD Research Development Neurosciences Advanced Imaging Research Center 47 New Scotland Ave., MC65 Albany, NY 12208 office: (518) 262-0810 fax: (518) 262-0802

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a small tkmedit issue
by Sebastian Moeller 04 Oct '05

04 Oct '05

Hi All, I recently tried to visualise the result of 10 mprage runs in one animal. Using the 20050921dev version of freesurfer (centos4_x86_64) mri_motion_correct2 went through smoothly. Since I scanned at 0.5mm^3 voxel size I unpacked the anatomicals into MGH instead of COR, trying to look at the result of the average result of the 10 scans at magnification of 2 resulted in funny looking artifacts. In the attached tiff file one can see two dorso-ventral edgers running through the slice, were the display seems to be off by some slices. Very prominent over the cerebellum where the blood vessels simply stop. I redid the unpacking and mri_motion_correct2 based averaging to produce SPM format output. This output produces the same artzefacts when view with tkmedit but looks okay when viewed with mricro. Please let me know, whether I can be of any help in this issue. Best Regards Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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reading Varian data files
by Renat Yakupov 03 Oct '05

03 Oct '05

Hi everybody, I have some data from a Varian 4T scanner. I tried mri_convert -it sdt on it, and it didn't work, complaining that it couldn't fine a header file. The data itself is in the following format: one big file, named "fid" which basically contains raw data, and an ASCI file name "procpar" which is like a header file. Does anybody have any experience with converting Varian data? Any suggestions what I could try to convert it? Thank you. Regards, Renat.

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analyze to bshort
by Mark Williams 03 Oct '05

03 Oct '05

Hi, Is there any way to transform images in spm analyze format to bshort? Thanks Mark

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matlab functions for reading sphere.reg files
by Darren Weber 03 Oct '05

03 Oct '05

Hi, are there any matlab functions for reading sphere.reg files? What is their format and content? Best, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." --Thomas Willis (1664), The Anatomy of the Brain and Nerves.

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control points
by Sasha Wolosin 03 Oct '05

03 Oct '05

Dear all, I am trying to add control points for a subject in order to improve normalization and skull stripping, but I found that the control points I added did not have much effect on the end result. I know control points should be added at points that the user feels sure are inside the white matter boundary, and that there should be about 20 spread out throughout the volume, but I am still uncertain as to how to choose them effectively. Should they be closer to the white/gray boundary? Or closer to the center? I believe I would be able to choose these points more effectively if I understood how FreeSurfer uses control points. Is it used as a high or low cut-off thresh-hold? Or is it more complex than that? Is location taken into account or is it just the intensity values that are used? Any help is greatly appreciated. Thank you, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Freesurfer October 2005