Freesurfer March 2005

freesurfer@nmr.mgh.harvard.edu

28 participants
35 discussions

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Skull Stripping Problem
by iag iag 04 Mar '05

04 Mar '05

2 1

thickness measures
by Kirk, Gregory 03 Mar '05

03 Mar '05

HI all, wrt useing freesurfer for obtaining cortical thickness there are the lh.thickness etc. and the theoretical paper in the citations, but I have not found things that would show me how to derive things like, average thickness for an individual, average thickness of a region or thickness at a point for an individual. I need it seems a way to interpret the two thickness files, i.e. mapping the numbers therin to a point on the geometry. thankx Greg

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Re: tkmedit's label files
by George Papadimitriou 03 Mar '05

03 Mar '05

Hi guys, I need to convert a label file into analyze, and see if I can import it to the Syngo as an ROI. How can I do this? I recall reading in an FS-FAST manual about a label2roi program. I don't see it in the standard nmr environment. I'd really appreciate your input. George P. On Wed, 2 Mar 2005, Ruopeng Wang wrote: > > Hi George, > > I have no idea what tkmedit's label file is. I never used tkmedit for > real. But I remember some time ago, someone, maybe Judith, converted one > to Analyze format, with help from one of tkmedit's developers (maybe > Doug). > > Ruopeng > > On Wed, 2 Mar 2005, George Papadimitriou wrote: > >> Hi Ruopeng, >> >> Are you familiar with tkmedit's label files? They are used to select an >> ROI. I would like to convert them into ANALYZE and import them into the >> Syngo. Have you done this before? What are your suggestions? >> >> Thanks, >> George P. >> >

2 4

(no subject)
by Harshad Shanbhag 03 Mar '05

03 Mar '05

Hi all, My earlier error was due to perl not properly configured. Thank you all for the help. However, on running recon-all -stage1 -subjid TEST, I am now getting the error message mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status Please help me out. Thank you, Harshad.

2 1

Error: Nu Correct
by Harshad Shanbhag 01 Mar '05

01 Mar '05

Hi all, I am trying to use FreeSurfer to overlay FSL data. On running the command $ recon-all -stage1 -subjid TEST I get the following error, Nu Intensity Correction Tue Mar 1 14:54:08 EST 2005 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=1.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc nu_correct: Command not found. ERROR: nu_correct I do have MNI Tools installed, in the freesurfer folder. Please let me know what I should do. Thank you. Harshad.

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Freesurfer March 2005