Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

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.

3 2

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

2 1

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)

2 1

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-----

1 0

ab blocked design analysis
by Tom Bayer 22 May '06

22 May '06

to analyze an ab blocked experiment, is it appropriate to run selfreqavg? I am analyzing data from a somatopy experiment, so the stimulus is not expanding or rotating but it is phasic. I analyzed it as an eccentric stimulus with positive value. Is this an appropriate choice? -tom

6 10

FreeSurfe NIFTI
by Doug Greve 19 May '06

19 May '06

I just wanted to let you know that I've modified the way FreeSurfer stores NIFTI1 files (these are the single .nii and .nii.gz files). The change is somewhat esoteric: the vox_offset is now 352 instead of 348. 352 is the NIFTI spec, so we were technically out of compliance before, though AFNI, FSL, and SPM did not seem to have a problem with it. 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

1 0

retinotopy starting with blanks
by Dahlia Sharon 18 May '06

18 May '06

Hi, I'm analyzing a retinotopy data-set in which each scan started with 2 TRs of a blank screen, and then proceeded to 8 cycles as usual. Is there any possibility to tell a retinotopy analysis to ignore these 2 TRs? Thanks! Dahlia. PS - I can't answer as to why these 2 blank TRs were put there.

2 1

FreeSurfer algorithms
by anthony gallo 18 May '06

18 May '06

Surfers, Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data.......maybe there are some papers that talk about this?? Anthony

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