Freesurfer

freesurfer@nmr.mgh.harvard.edu

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using matlab loops for MRIwrite
by corinna bauer 11 Aug '10

11 Aug '10

Is there a way to use a loop with MRIwrite such that each subject's output has a different name? Thanks, Corinna

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orient_mri
by Prapti Gautam 11 Aug '10

11 Aug '10

Hi, I'm trying to use orient_mri to orient a volume that is displaying as an axial rather than a coronal volume. According to the instructions, I need to see 4 views and be able to rotate the loaded volume - but I only see one window.. do you know why this is ? there wasn't a error message as such , but the volume isn't being displayed as it should I think .. The command I use is : orient_mri -volume orig.mgz I'm using a linux ubuntu with freesurfer version 4.3 thanks, Prapti

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segmentation output from freesurfer version 4.0.2
by Keslerwest, Marilyn 10 Aug '10

10 Aug '10

Dear Freesurfer experts, We have aparc+aseg.mgz segmentation and other files from Freesurfer version 4.0.2 . We do not have the original images, and so cannot easily reprocess with a later version. I have looked at the release notes. I saw that version 4.0.2 has a problem with the estimated Total Intracranial Volume calculation and I have heard that there may be other issues. So I am wondering if you think it would be problematic to use these aparc+aseg.mgz files for overlay with the functional images for an ROI analysis. Thank you, - Marilyn ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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Increasing Color Bar colors
by Jeff Sadino 10 Aug '10

10 Aug '10

Hello, I am interested in learning how to increase the number of colors that show up on the tksurfer color bar. Right now, I pretty much only get two or three colors at a time - blue, red, and yellow. I see pictures in publications that show the whole rainbow: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743662/?tool=pubmed also http://jsadino.awardspace.com/fs.html Can anyone please explain the process to me of how to get this increased color range on the tksurfer maps? Thank you very much, Jeff Sadino

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Cortical Thickness of a Volume-defined ROI
by efrat kliper 10 Aug '10

10 Aug '10

Dear FreeSurfer expert I am trying to create a mask for the right hemisphere frontal lobe cortex in order to calculate the mean cortical thickness for this specific ROI. I am using the following commands: To create a mask for the specific region: mri_binarize --i /mri/aparc+aseg --match 2028 --match 2027 --match 2003 --match 2024 --match 2018 --match 2020 --match 2019 --match 2014 --match 2032 --match 2002 --match 2026 --o /mri/rh_frontal_ctx.mgz But I am not sure what the next step is - I tried to follow this link: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness(Cortic… Thickness of a Volume-defined ROI) fslregister --s fsaverage --mov /mri/T1.mgz --reg T1_to_fsaverage.dat but I am not sure if that is the correct way, and also my ROI in the fsaverage subject volume is not perfectly matched to what I expect it to be - how can I fix that? They are very different. I also tried the mri_tessellate command to create surface by tessellating given input volume: mri_tessellate /data/Temp_efrat/subjects/TB_281_test/mri/rh_frontal_ctx_1.mgz -a 2028 2027 2003 2024 2018 2020 2019 2014 2032 2002 2026 frontal_ctx_test I get this massage: changing type of input volume to 8 bits/voxel... $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ slice 110: 431 vertices, 495 faces slice 120: 2986 vertices, 3215 faces slice 130: 6636 vertices, 7037 faces slice 140: 12817 vertices, 13506 faces slice 150: 22361 vertices, 23291 faces slice 160: 32454 vertices, 33549 faces slice 170: 44058 vertices, 45346 faces slice 180: 56174 vertices, 57633 faces slice 190: 67020 vertices, 68612 faces slice 200: 75820 vertices, 77402 faces slice 210: 78847 vertices, 80236 faces slice 220: 78900 vertices, 80278 faces slice 230: 78900 vertices, 80278 faces slice 240: 78900 vertices, 80278 faces slice 250: 78900 vertices, 80278 faces using the conformed surface RAS to save vertex points... writing 2028 using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; But I can not find the output file of that command. And then to calculate the thickness of the frontal cortex by using the mris_anatomical_stats TB_281_test rh -t frontal_ctx_test I am a little confused, I will be grateful if you can help me with that. Thanks a lot Efrat <Freesurfer(a)nmr.mgh.harvard.edu>

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Red Hat vs. CentOs
by dahlia＠nmr.mgh.harvard.edu 10 Aug '10

10 Aug '10

Hi, I'd like to make sure that a Dell desktop with pre-installed RHEL would work seamlessly with Freesurfer, equivalent to CentOS. Is this correct? Thanks, Dahlia.

4 4

File Format for talairach.m3z
by Soon Hock Wei 10 Aug '10

10 Aug '10

Dear All: I am a new user of FreeSurfer and I am wondering what is the file format for talairach.m3z (i.e. the output of mri_ca_register)? I couldn't find this information in FreeSurfer Wiki. In addition, I would like to know how can I use this talairach.m3z to check the accuracy of non-linear mapping to the atlas space? And if I wanted to replace this non-linear transform (i.e. talairach.m3z) by another non-linear transform (without affecting the other process flow), how should I do that? Appreciate if anyone could kindly show me some guidance. Thanks! Best Regards, Soon National University of Singapore

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surface-based aal template
by Zhangyuanchao 10 Aug '10

10 Aug '10

hi, expert I need a surface-based aal template which is compatible with freesurfer surface files. Is there any way I can obtain such a surface-based aal template? Thanks!

1 0

region seeding and growing
by Eriksen, Jeffrey (Portland) 09 Aug '10

09 Aug '10

I have looked at the web site and gone through much of the available documentation (without downloading the installer yet) and cannot find if FreeSurfer offers low-level region seeding and growing capabilities. Anyone able to confirm or deny such a feature? Thanks, Jeff Eriksen, PhD Senior Research Associate Oregon Brain Imaging Research Lab (OBIRL) Portland VA Research Foundation kjeffrey.eriksen2(a)va.gov 503-220-8262, x54117

2 1

[freesurfer] a puzzling installation error
by Glen Lee 09 Aug '10

09 Aug '10

Dear freesurfer experts, I'm running into installation failure and can't quite figure this out (I'm a novice Linux user too). It complains there is no such file or directory although I've downloaded the file and move that to the usr/local directory, so there clearly is the file. Would anybody help me how to resolve this issue? Below is the error message and platform info. Many thanks! -GL ------------------------------------------------------------------------------- glen@ubuntu:/usr/local$ uname -a Linux ubuntu 2.6.32-24-generic-pae #39-Ubuntu SMP Wed Jul 28 07:39:26 UTC 2010 i686 GNU/Linux. tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/surf/ tar: freesurfer/average/surf: Cannot mkdir: No such file or directory freesurfer/average/surf/lh.sphere.reg tar: freesurfer/average/surf/lh.sphere.reg: Cannot open: No such file or directory freesurfer/average/surf/rh.sphere.reg tar: freesurfer/average/surf/rh.sphere.reg: C

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