Freesurfer

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7 participants
30057 discussions

troubles with monkey brains (inflate)
by Sebastian Moeller 22 Feb '06

22 Feb '06

Dear all, at the moment I am struggling with flattening monkey anatomical scans. Specifically I manually got to the point where I get a wm.mgz and now I want to inflate it. My instructions refer to using csurf, which does not like my mgz volumes and is deprecated IIRC, the alternative is hooking my data into the recon-all pipe-line. But that fails as I do not have any aseg.mgz (does the segmentation work for monkeys?). So any advice on how to proceed with the processing? Ahoi & Thanks Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 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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file paths in mgz headers
by Glenn Lawyer 22 Feb '06

22 Feb '06

Hi, We like to structure our work by putting all scans into a batch account and doing recon-all -autorecon1 -autorecon2. We then transfer the scans to our individual accounts to check the quality before running the rest of the processing stream. This creates a small problem, in that the full path to the talairach.xfm is saved as part of the mgz volume. When we move the scan from the batch account to the user account, this path is no longer valid. We can fix this by using mri_add_xform_to_header, as per msg02241 on the mailing list (Doug Greve, 27 Jan 2006). What we are wondering is if the mgz header has any other path-dependant information that we would need to update in the scenario such as above, where scan workup and group analysis processing can take place over multiple file locations? +glenn

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Re: tcl script - rotate and save graphics (Darren Weber)
by Glenn Lawyer 22 Feb '06

22 Feb '06

Hi, Darren, I once made an animated gif of a rotating brain showing some freesurfer results. I did this with two scripts. The first is a tcl script that was passed to tksurfer; it rotates the brain and saves the resulting images. The second is a shell script that uses imagemagik to convert all of the resulting rgb images into one animated gif. I am attaching the scripts. Please be aware, however, that the tcl script isn't very elegent. I'm actually a little embarassed by it. Also, both scripts are set up for my file system, you will need to edit a few of the settings to get them to work for you. The tcl script is based on an earlier one I saw on the mailing list, I think it was Doug Greve's, but I'm not sure. I don't give credit in the script itself, sorry for the oversight! +glenn -- It is not an aesthetic process; it's a form of magic that interposes itself between us and the hostile universe, a means of seizing power by imposing a form on our terrors as well as on our desires. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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problems with wm surface
by Martin Ystad 22 Feb '06

22 Feb '06

Hi, I've just installed the newest centos-dev version. I did a rerun on some of my subjects, and in one particular subject the white matter orig-surface didn't follow the white matter volume at the right hemisphere. It looks like the surface takes some 'shorcuts' passing through gyri and over sulci. This only happens in the right hemisphere, and it didn't happen in the previous version. (I've attached an image to illustrate) Do you have any idea what causes this, and if so, what I can do to fix it? Also, I'd like to know if the talairach-conversion has any significant impact on the final result, so that I should try to obtain the lowest 'Final objective function value' by applying the tecniques suggested in your tutorial. Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway.

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label surface co-registrations
by Darren Weber 21 Feb '06

21 Feb '06

Hi Bruce etal., I have a label defined for the rh. Is there a way to automatically locate this label in the homologous lh location, using the surface coregistration methods of freesurfer? Best, Darren -- Darren L. Weber, Ph.D. Visiting 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 (The Anatomy of the Brain and Nerves, 1664)

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intensity normalization
by dominick＠bu.edu 21 Feb '06

21 Feb '06

Hi, I had been having a lot of trouble with the skull stripping in the newest dev version (it was taking off the top half of the head and leaving head and skull on the bottom half). I was able to fix this by redoing the intensity normalization step from autorecon1 using control points. My question is - In the brains where I did not have a problem with skull stripping, but after autorecon1 I have white matter intensity values below 110, should I redo intensity normalization with control points on them as well? Thanks! Kelli

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Viewing GCS / Atlas files
by Timothy R Jarvis 21 Feb '06

21 Feb '06

I've searched the WIKI and didn't see any instructions on how to view the following files: average/lh.atlas2002_simple.gcs - lh atlas average/rh.atlas2002_simple.gcs - rh atlas Is there a utility provided to do this, or can someone tell me what the file format / contents of these files is? Thanks --------------------------------------- Timothy R. Jarvis --------------------------------------- Graduate Research Assistant International Neuroimaging Consortium VA Medical Center 612-467-2619 http://www.neurovia.umn.edu ---------------------------------------

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mris_preproc file missing in my freesurfer package.
by Goradia, Dhruman D 20 Feb '06

20 Feb '06

Hi all, I have the following freesurfer version: OS: Mac OS X Platform: Tiger Release type: dev The mris_preproc file is missing. I would appreciate if some one can email me this file. Thank you. Dhruman.

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Output of mris_anatomical_stats
by Goradia, Dhruman D 17 Feb '06

17 Feb '06

Hi, The output of function "mris_anatomical_stats" contains the following measurements: integrated rectified mean curvature, integrated rectified Gaussian curvature, folding index and intrinsic curvature index. Can someone please give me a brief explanation of what these measurements are or suggest some reading material. -Dhruman Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213 Phone: 412-586-9017

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-legacy flag
by Vasanth Pappu 13 Feb '06

13 Feb '06

Hi, I started to run an old subject through autorecon1 and 2. I used the -legacy flag. However, I still got the error below, saying that I need some *mgz files in the orig/ directory. I thought -legacy would do this conversion. The orig/ had a COR volume, but the error said to have a 001.mgz and a 002.mgz. I tried to convert the dicoms with -i, but it would not write to the existing directory: recon-all -i /autofs/space/solo_004/users/dcm/CARG29/cdrom/03051411/21527384 -i /autofs/space/solo_004/users/dcm/CARG29/cdrom/03051411/21526253 -subjid CARG29_recon INFO: SUBJECTS_DIR is /autofs/space/biggs_008/users/vasanthp/NHS ERROR: /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon exists So, I ended up converting the dicoms in another directory, copied the 001.mgz and 002.mgz to the CARG29_recon/, and then started to run recon-all -autorecon1 and 2. Is there a simpler way to do this? Thanks, Vasanth [biggs:mri] (nmr-dev-env) recon-all -subjid CARG29_recon -autorecon1 -autorecon2 INFO: SUBJECTS_DIR is /autofs/space/biggs_008/users/vasanthp/NHS Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev -rwxrwx--- 1 vasanthp cagn 76436 Feb 13 16:22 /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/scripts/recon-all.log Linux biggs 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 14:49:37 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/dev Previous: /space/windu/6/users/freesurfer_cenagn/freesurfer_dev #-------------------------------------------- #@# MotionCor Mon Feb 13 16:23:34 EST 2006 ERROR: no run data found in /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/mri. Make sure to have a volume called 001.mgz in /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux biggs 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 14:49:37 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Feb 13 16:23:34 EST 2006 --

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