Freesurfer February 2006

freesurfer@nmr.mgh.harvard.edu

40 participants
52 discussions

paint, mri_vol2surf, paint-sess
by Don Hagler 23 Feb '06

23 Feb '06

I tried painting to a surface created with the new recon-all (using paint or mri_vol2surf (version 1.22 2005/07/05)), and it seems that the surrfaces are not being read correctly (the data in the w file has the speckled appearance you get when the vertex numbers are wrong). I posted a message before about my fieldsign code not working on the new surfaces and Bruce Fischl said this about the different surfaces (i.e. orig, smoothwm, inflated, etc.): "check the # of vertices etc... with mris_euler_number (or mris_info). Make sure they all are the same. The file sizes aren't necessarily the same any more as they contain additional info, but the # of vertices etc. should be invariant." So are paint and mri_vol2surf still supported under the current distribution of MGH FreeSurfer? Are there newer versions out there? Or is everyone using paint-sess these days? By the way, what was done to the format of the surfaces? What additional info do they contain? Is there documentation or posted code on how to read the new surfaces?

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tkregister2 talairach target
by Doug Greve 23 Feb '06

23 Feb '06

Starting tomorrow (Fri), those using nmr-dev will notice a different talairach volume when checking/editing your talairach registration with tkregister2, eg, tkregister2 --fstal --s bert Previously, it used $SUBJECTS_DIR/talairach/mri/orig.mgz Now, it uses $FREESURFER_HOME/average/mni305.cor.mgz The old one was an average that was created a long time ago. The new one is the actual MNI 305 template that is used during automatic talairach registration done in recon-all. We are changing the target because it is better to use the actual template than a surrogate. We are changing it now in anticipation of the (soon) new freesurfer release (!). You should not need to modify your talairach.xfm based on the new target, as the true template and the surrogate are quite close to each other. You can see by comparing the old and new by running: tkregister2 --fstal --s talairach (you will not be able to save any edits :). doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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mghWrite error
by Nguyen, Thang Q 23 Feb '06

23 Feb '06

Hello all, I have a few scans I need to convert using mri_convert but I receive this error: writing to 2.mgh... mghWrite(2.mgh, -1): could not open file ERROR: failure writing 2.mgh I can convert other images from the same scanner, same subject, same header without any problems but the few that I have recently tried to convert have this issue. I can view the images in tkmedit so I don't believe there is an issue with the images themselves. What does this error mean and how can I override it? Thank you all for your input, Thang Nguyen ------------------------ Thang Nguyen Biomedical Informatics Research Network Psychiatry and Human Behavior - Brain Imaging Center University of California, Irvine

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label_child memory erro
by hwier＠uchicago.edu 23 Feb '06

23 Feb '06

Hi, I'm running freesurfer (version 0.9, 33y) and I'm trying to run the label_child script I found in the bin directory, however I'm getting the following error(where my subject directory is called 205): ---------------- Command Line: > label_child 205 ---------------- Output: using gca /opt/freesurfer_alpha/average/talairach_children_tl_b.gca to label thin temporal lobe... using /nfs/raidzone/data/NL-GCS/subjects/freesurfer//205/mri/brain to mask final labeling... reading 1 input volumes... reading classifier array from /opt/freesurfer_alpha/average/talairach_children_b.gca... GCAread(/opt/freesurfer_alpha/average/talairach_children_b.gca): couldn't expand gcs to 286990032 Cannot allocate memory ------------------- My computers' resources (from /proc/meminfo) are: MemTotal: 4148928 kB MemFree: 871196 kB Can my computer handle running label_child? Am I just calling something incorrectly? Is there anything I could try to change in order to get label_child to run? Thanks, Helen.

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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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Freesurfer February 2006