Re: [Freesurfer] FSL/Freesurfer

2006-03-21 Thread Clifford A. Smith, PhD
006 12:28:43 -0500 > To: "Clifford A. Smith, PhD" <[EMAIL PROTECTED]> > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] FSL/Freesurfer > > Clifford, > > After sourcing SetUpFreeSurfer.csh, but before starting FSL, type this: > > unsetenv TCLLI

[Freesurfer] FSL/Freesurfer

2006-03-21 Thread Clifford A. Smith, PhD
Title: FSL/Freesurfer I believe that I have read a post on this in the past, but I was unable to run a search.  I have FSL configured to startup in X11 without a problem.  Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem.  But FSL will not work after I have ran the source S

Re: [Freesurfer] Newest stream

2006-02-08 Thread Clifford A. Smith, PhD
points to help define the white matter intensity?    -- Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893 From: Doug Greve <[EMAIL PROTECTED]> Date: Tue, 07 Feb 2006 15:57:15 -0500 To: "Clifford A. Smith, P

[Freesurfer] Newest stream

2006-02-07 Thread Clifford A. Smith, PhD
Title: Newest stream With the most recent release, does the skullstripping take place with brainmask.auto.mgz  and brainmask.mgz?  After completing recon-all –autorecon-all I checked brain.mgz. I had some frontal areas missing, so ran  recon-all -skullstrip -wsthresh 30.  Brainmask.mgz looks goo

Re: [Freesurfer] Simple ? about T1.mgz

2006-01-12 Thread Clifford A. Smith, PhD
> Date: Thu, 12 Jan 2006 17:12:31 -0500 (EST) > To: "Clifford A. Smith, PhD" <[EMAIL PROTECTED]> > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] Simple ? about T1.mgz > > Hi Cliff, > > there's an interim dev version in which T1 is created with a

[Freesurfer] Simple ? about T1.mgz

2006-01-12 Thread Clifford A. Smith, PhD
Title: Simple ? about T1.mgz I’ve been going over the tutorials, but my question remains – is T1 skull stripped?  It seems to check skull stripping brain.mgz is loaded as the main volume with T1.mgz as the aux.  Flipping back and forth (control 1/control 2) is used to check the stripped brain.mg

[Freesurfer] Two questions.

2005-09-22 Thread Clifford A. Smith, PhD
Title: Two questions. First, I have successfully completed recon-all on my Mac.  I created the subject directories using mksubjdirs prior to running recon-all.  After running recon-all the files are all in the mri folder, and the respective folders (eg brain, T1, and filled) remain empty.  Is

Re: [Freesurfer] Fix_topology error

2005-09-02 Thread Clifford A. Smith, PhD
Mac (but not on any of the > Linux platforms), and are currently chasing it down. > > Nick > > > On Thu, 2005-09-01 at 16:15 -0500, Clifford A. Smith, PhD wrote: >> Ran recon-all ­autorecon1 without a problem. >> >> Ran recon-all ­autorecon2 with the followi

[Freesurfer] Fix_topology error

2005-09-01 Thread Clifford A. Smith, PhD
Title: Fix_topology error Ran recon-all –autorecon1 without a problem. Ran recon-all –autorecon2 with the following error being produced with mris_fix_topology.  Any suggestions on proceeding?   Cliff Fix Topology rh Wed Aug 31 19:49:23 CDT 2005 /Users/Shared/freesurfer/subjects/00139/scripts

[Freesurfer] Recon-all followup

2005-08-30 Thread Clifford A. Smith, PhD
Title: Recon-all followup Following Yuan-Fen Kuo’s suggestion, I added a # at line 275 in recon-all.  Recon-all –stage1 now proceeds until it crashes with the following: Intensity Normalization Tue Aug 30 12:47:03 CDT 2005 /Users/Shared/freesurfer/subjects/00139/mri mri_normalize orig.mgz T1.mg

[Freesurfer] Recon-all question

2005-08-30 Thread Clifford A. Smith, PhD
Title: Recon-all question I’ve installed Freesurfer on Mac running Tiger.  Am able to run mri_convert to attain 001.mgz and view with tkmedit without a problem.  Can run recon-all –help and attain the help files, but running recon-all –subjid -all (or autorecon1) –mgz does not produce any image