Freesurfer April 2004

freesurfer@nmr.mgh.harvard.edu

18 participants
14 discussions

non-primate brains
by Geoffrey Aguirre 29 Jun '04

29 Jun '04

Free surfers -- I am collecting data from dogs. Any advice regarding passing this data through the system? I have a couple of specific questions: 1) Should I acquire data with voxel sizes smaller than 1mm, given that the brain is much smaller? How would I tell free-surfer to operate with this higher resolution data? 2) So far, automated skull stripping has been a failure, even with definition of a "seed point" in the white matter. The routine strips away the brain around the seed point, leaving a large chunk of scalp and muscle with a bit of cortex attached. Any thoughts on how to get this going? Thanks in advance for any help, Geoff -- Geoffrey Karl Aguirre, M.D., Ph.D. University of Pennsylvania Center for Cognitive Neuroscience 3815 Walnut Street Fax: (215) 898-1982 Philadelphia, PA 19104-6196 mailto:aguirre@neuro.med.upenn.edu http://ccn.upenn.edu/~aguirre

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updated tkmedit won't run..
by Wietske Van Der Zwaag 05 May '04

05 May '04

Dear Freesurfers, I've just updated my freesurfer to the 20040218 version, but now I am no longer able to run the tkmedit program. I've tried the tkmedit.static version too, but with the same result (ie none) The log file says this: /usr/local/freesurfer/bin/Linux/tkmedit blobby T1 -csurf Command Finished Does anybody know what to do about this? I don't think anything's wrong with the videocard, as I was able to run the older version of tkmedit. Thank you, Wietske

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Seg fault during wm_fill
by Geoffrey Aguirre 28 Apr '04

28 Apr '04

Folks -- I'm working with a dog brain. With the help of Denis Fize, I've "tricked" freesurfer into treating my 0.47 mm voxels as 1 mm voxels, and I have manually stripped the skull. I used the automated routine to segment white matter and then manually erased the brainstem and cerebellum. Now, however, when I try and apply the automated white matter fill routine, the operation fails with "Segmentation Fault" after several minutes of processing. I've provided left and right hemisphere seed points, as well as a callosal seed point. This is a fairly unusual data set, but I would appreciate any advice... Thanks, Geoff -- Geoffrey Karl Aguirre, M.D., Ph.D. University of Pennsylvania Center for Cognitive Neuroscience 3815 Walnut Street Fax: (215) 898-1982 Philadelphia, PA 19104-6196 mailto:aguirre@neuro.med.upenn.edu http://ccn.upenn.edu/~aguirre

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How to get each value for total out and inner cortex surface area
by Akemi Tomoda 28 Apr '04

28 Apr '04

Dear list, According to the results by running FS in our subjects, I have come to realize that the cortical surface area and gray-matter volume shrinks, while the cortical thickness tends to increase with a highly localized area of cortical thickening in the left hemisphere. To my knowledge, these two variables (area, thickness) can not possibly be independent. So there must be a relationship because volume = area * thickness. In order to test it statistically and look into the problem of interaction between thickness and area, I'd like to get the values of total out cortex surface area and total inner cortex surface area, separately. I know FS use the white surface for surface area from the past ML (Pial Surface). I was wondering how I can get each value for out and inner cortex surface area. Any suggestions are very welcome. Akemi Developmental Biopsychiatry Research Program McLean Hospital atomoda(a)mclean.harvard.edu Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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subcortical parcellation
by Frederic Dick 28 Apr '04

28 Apr '04

Hi all are there any plans to release the subcortical parcellation as part of freesurfer? Or is it in another set of tools? Or is it still in-house only? Thanks! Fred

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need clarification of analyze 7.5 format orient value
by Yasunari Tosa 18 Apr '04

18 Apr '04

I need the clarification of analyze 7.5 format in sagittal flipped case. I just found that it is different from the one I used for freesurfer. I used Graham version from his web site: wideman-one.com/gw/brain/analyze/formatdoc.htm has *hist.orient* *Mayo name* *Voxel[Index0, Index1, Index2] * *Index0* *Index1* *Index2* 0 (default) transverse unflipped R-L P-A I-S 1 coronal unflipped R-L I-S P-A 2 sagittal unflipped P-A I-S R-L 3 transverse flipped R-L A-P I-S 4 coronal flipped R-L S-I P-A 5 sagittal flipped P-A S-I R-L Note: Index0 is fastest-varying (innermost-nested) index, Index2 the outermost. Index0..Index2 are often called X, Y, Z, but I am trying to avoid confusion with spatial coordinates. I found that http://nifti.nimh.nih.gov/dfwg/nifti_revised.html has * /vs./ qform_code*: The ANALYZE-7.5 format indicated 3D orientation with the 1 byte code orient, which was to be interpreted as 0 = transverse-unflipped R?L P?A I?S 1 = coronal-unflipped R?L I?S P?A 2 = sagittal-unflipped P?A I?S R?L 3 = transverse-flipped R?L A?P I?S 4 = coronal-flipped R?L S?I P?A 5 = sagittal-flipped P?A I?S L?R Note that the second and third axis of "sagittal flipped" are flipped ;-) Tosa -- Yasunari Tosa, Ph.D. R&D Engineer email: tosa(a)nmr.mgh.harvard.edu Mass. General Hospital NMR Center phone: Building 149 13th Street fax : Charlestown, MA 02129

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inside or outside the brain
by Daniel Goldenholz 16 Apr '04

16 Apr '04

Hi. I have a math question. Suppose that I read a non-inflated brain surface using the matlab function "read_surf". Suppose further I have a single point which is in the same mri coordinate system as this surface. My question is this: what is a smart way to figure out if that single point is INSIDE or OUTSIDE the 3D volume called "brain" bounded by the surface I read in? Thanks, -- Daniel Goldenholz -----------------------------------------------------

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problem with white matter fill
by Wietske Van Der Zwaag 15 Apr '04

15 Apr '04

Hello, When we tried running the white matter fill procedure on the example data, we kept encountering these error messages. The line 'MRIvoxelToTalairachVoxel: unsupported slice direction -1' seems to be repeated for every voxel in the volume. Can you tell me what this errormessage is about and what's wrong? We tried running the white matter fill from the commandline or with the gui, and get the same result. Wietske /usr/local/freesurfer/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /arthur/data_local/subjects/blobby/mri/tmp/ponscall.dat /arthur/data_local/subjects/blobby/mri/wm /arthur/data_local/subjects/blobby/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /arthur/data_local/subjects/blobby/mri/tmp/ponscall.dat... reading input volume...done. searching for cutting planes...MRIvoxelToTalairachVoxel: unsupported slice direction -1 MRIvoxelToTalairachVoxel: unsupported slice direction -1 MRIvoxelToTalairachVoxel: unsupported slice direction -1 MRIvoxelToTalairachVoxel: unsupported slice direction -1 MRIvoxelToTalairachVoxel: unsupported slice direction -1 MRIvoxelToTalairachVoxel: unsupported slice direction -1

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Brain skull size
by Akemi Tomoda 15 Apr '04

15 Apr '04

Dear list, Is there a way to get brain skull size of subjects using FreeSurfer? I already have got Brain Size (cm3) from the output of mri_strip_skull, but my guess is that it would be different from the skull size. I'd be most grateful if anyone could let me know of the way of outputting these values. Thanks in advance, Akemi Developmental Biopsychiatry Research Program McLean Hospital of Harvard Medical School atomoda(a)mclean.harvard.edu Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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Linux mri_watershed update fixed
by Kevin Teich 14 Apr '04

14 Apr '04

Okay, there is a fixed Linux binary available for the mri_watershed update: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.… -- Kevin Teich

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Freesurfer April 2004