Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30050 discussions

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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Fix for mri_watershed
by Kevin Teich 14 Apr '04

14 Apr '04

There's a new version of mri_watershed available. The fix is to eliminate s problem with the WM value. The previous version sometimes used the pon area for the WM value. Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.… Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Darwin.tar… -- Kevin Teich

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mris_flatten usage
by Jonathan Polimeni 03 Apr '04

03 Apr '04

hello all! i have a fast question regarding the usage of mris_flatten: what are the available command line options? the usage message displayed by mris_flatten only lists the "-w" and "-distances" options, but i also know of the "-p" option, and there was an earlier posting that mentioned a "-s" option as well. does the option "-p <N>" repeat the flattening procedure N times by feeding the output of flattening k into the input of flattening k+1? does the "-s 1" option turn the scaling off? is this a binary flag? is the default then equivalent to passing "-s 0"? thanks in advance! -jon

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error
by Mary Fitzsimons 02 Apr '04

02 Apr '04

Need help! In csurf when I click on volume or surface to display images the following error message arises the same thing happens if I try to use tkmedit/tksurfer from the command prompt. Error while loading share libraries: libtk8.3.so:cannot open shared object file: no such directory I cannot locate libtk8.3.so on my computer so I looked up RPMfind on the net a download is available but it leads to a broken link can anyone send me this library? >From the websearch I found that libtk8.3.so is part of a graphical toolkit TCL scripting language. Do I need to have TCL on my machine? Are there any other specific requirements to run Freesurfer? Many thanks Mary Fitzsimons

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Looking for correct coordinates
by Daniel Goldenholz 31 Mar '04

31 Mar '04

Hi freesurfer folks. I have a pair of inflated brains that I'd like to work with in matlab. I found a nice function called "read_surf.m" which works very well. But I noticed that the two hemispheres cannot be viewed at the same time, because their locations overlap! I pushed one to the left and one to the right by an arbitrary amount, and this looked a bit better. But I was hoping to put the position of the inflated brain in the correct spot so that I could correlate MEG info with these surface files. What else do I need to know about positioning these brain surfaces? Thanks -- Daniel Goldenholz -----------------------------------------------------

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remote desktop turns blue?
by Nguyen, Thang Q 31 Mar '04

31 Mar '04

Hello all, I don't know if anyone has had this problem before but when I remote desktop into a PC running freesurfer (csurf), the brain image in tkmedit turns blue. In addition, tksurfer doesn't load. When I relog on to the PC, I can reload tkmedit and it works fine. Here are some specifications: Running freesurfer-20030724 Remote desktop with windows XP Pro to another windows XP Pro PC Running Reflections X on the PC desktop Running RedHat v9.0 on the compute nodes In addition to all this trouble, after editing in tkmedit and creating a new surface, the surface doesn't reflect the new changes. This hasn't happened before. Does anybody have any ideas on what contributes to these problems? Thanks, Thang ------------------------ Thang Nguyen Psychiatry and Human Behavior - Brain Imaging Center University of California, Irvine This e-mail/fax message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail/fax and destroy all copies of the original message.

3 2

Pial Surface
by Keyma Prince 30 Mar '04

30 Mar '04

When you look at the values that are produced by mris_anatomical_stats for surface area, are these values the same as pial surface area? Is the pial surface the same as the inflated surface? -Keyma

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