Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

updated tutorial and data
by Nick Schmansky 26 May '06

26 May '06

Freesurfers, An updated Freesurfer tutorial is now online at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial and the data that accompanies it (processed by stable v3.0.2) is available through: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data The outline is setup for a two-day course (to align with tutorial sessions typically found at a conference). Each of the four sessions should take no more than 90 minutes to complete. Comments and suggestions are appreciated. The Freesurfer team

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troubleshooting
by Amanda Dow 26 May '06

26 May '06

I ran one of my brains through recon-all and the skull strip and talairach were normal. When I checked the white matter edits with tkmedit, the right hemisphere wm and pial surface lines are including some of the left hemisphere, and the right temporal lobes are not included as white matter or in the pial surface. I thought it may be a tailarach problem, but it looks normal. Any suggestion on what could be wrong. I may try using control points and re-running it with <recon-all -autorecon2-cp...> Thanks!

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colortable
by Satrajit Ghosh 26 May '06

26 May '06

1. Is there a matlab function to read the colortable from an annot file? 2. Is there a reason why several of the annotvalues generated by the classifier using rh.atlas2005_simple.gcs do not have corresponding names in surface_labels.txt? I remember there was a release where there was a separate colortable for that atlas, but it doesn't exist in the current download, so I was assuming they have been merged into a single file. Thanks, Satra

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scalp surfaces - mri_watershed vs betsurf
by Darren Weber 25 May '06

25 May '06

Dear Bruce, Steve, et al, have you compared the output of mri_watershed with betsurf? I ran a T1 volume through mri_watershed with the -surf output options. I also ran the same volume through betsurf. When comparing the two volumes, I specified an offset of -128 for the betsurf output. I expected a close correspondence between these surfaces. There is a slight rotation difference (see image attached). Have you seen this before? Steve, is there some reason the betsurf output could be rotated? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 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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unable to run mc-sess with bert dataset
by Olivier Piguet 25 May '06

25 May '06

Good morning, I recently installed the new version of FreeSurfer and have been re-familiarising myself with the steps/procedures. I followed the FreeSurfer and FsFast tutorial which went fine until I tried the step described in the FsFastTutorial/700: Motion correct the data. When I ran the command: mc-sess -sf sessid -df sesspar I received the following error message: Logfile is /home/olivierp/BERT_TUTORIAL_ANALYSES/log/mc-bert-functional-bold.log ------------------------------------------- /home/olivierp/FreeSurfer_tutorial/bert-functional RunList: 007 008 009 Targ Stem is 007/f ------- ************************** ----------- ------- Motion Correcting Run 007 ----------- ------- ************************** ----------- sess = bert-functional Fri May 26 08:27:34 EST 2006 mc-afni -i 007/f -o 007/fmc -t 007/f -toff 0 -ipr 3.12500000000000000000 -bpr 6. 00000007484366104649 -TR 2 ERROR: cannot find AFNI command to3d Any help/suggestion on how to solve this problem would be greatly appreciated. Olivier Piguet -- Olivier Piguet, Ph.D. Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia

2 1

smoothing kernel
by Sasha Wolosin 25 May '06

25 May '06

Dear all, In group analysis, how should I determine which value to use for the Gaussian fwhm smoothing kernel? Is there a recommended number? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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analyze format
by Chacko Cherian 24 May '06

24 May '06

Hello, I am having some trouble in running "Analyze" format images on freesurfer.Could someone please guide me on how to run images on this format.. THanx Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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can we use mri_strip_skull with .mgz volumes?
by Darren Weber 24 May '06

24 May '06

Hi, I've noticed that mri_strip_skull and mri_make_bem_surfaces are not working with .mgz files. They look for COR-.info and fail if it doesn't exist. Best, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 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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automated ROI extraction for overlays
by Nguyen, Thang Q 23 May '06

23 May '06

Hello all, This may be a newbie question but I couldn't find any information relating to automated overlay data extraction on Freesurfer. I tried searching the wiki page and the email archives with no luck. I have already used tkregister2 to align the freesurfer volume and the functional volume. I was wondering if there was an automated method of extracting the functional overlay values based on the Freesurfer parcellation atlas and it's thickness values. Thank you for your help, -Thang

2 1

recon-all for brain.tri?
by Darren Weber 23 May '06

23 May '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 It seems that recon-all does not output <subjid>/bem/brain.tri the tesselation of the inner skull. What is the latest utility for generating scalp, outer, and inner skull surfaces using freesurfer? Best, Darren - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 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) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFEc4XgxaCYN7qs0v4RAhd5AJ405YPpqHALLqhPDoNydgyb9pVtsQCgi1JF wQpDmdRFA9etoVU8OT6y1ZQ= =bRmY -----END PGP SIGNATURE-----

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