[Freesurfer] FS recon-all issue "if: missing file name"

2019-06-02 Thread Kavinash Loganathan
External Email - Use Caution Dear freesurfer, I am following the installation test as suggested ( http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall/) and am currently stuck at example 2. When I ran recon-all, I got the output: "if: missing file name". I noticed this has

Re: [Freesurfer] FS recon-all issue "if: missing file name"

2019-06-02 Thread Greve, Douglas N.,Ph.D.
can you send the command line and full terminal output? Also, when you run it again, put -debug as the first argument. It will create a huge amount of terminal output, but it will be helpful for diagnosing the problem On 6/2/2019 3:57 AM, Kavinash Loganathan wrote: External Email - Use

Re: [Freesurfer] selxavg3-sess failed

2019-06-02 Thread Greve, Douglas N.,Ph.D.
It does not look like the error was captured in the log file. Can you send the full terminal output? On 6/2/2019 5:02 AM, starxifd wrote: External Email - Use CautionIt Hi, FS experts I got into trouble when running ’selxavg3-sess’ with a session id file. All sessions specified

[Freesurfer] Cluster-wise multiple comparison correction

2019-06-02 Thread Jacobs, H (NP)
External Email - Use Caution Hi all! I would love to use the cluster-wise multiple comparison correction method in FS 6.0 for our PET data (in fsaverage space and smoothed). However, since we have some complex models, I did the statistical analyses in R and then converted this t

[Freesurfer] multi-slice timing correction

2019-06-02 Thread Joseph Dien
External Email - Use Caution Hi Doug, I’m happy to see that FreeSurfer6 provides enhanced support for slice timing. I’m trying to run it on some multi-slice data. May I ask you for some guidance on how to use the new preproc-sess options? As I understand it, I would specif

Re: [Freesurfer] Tracula error -path

2019-06-02 Thread Yendiki, Anastasia
Hi Lorenzo - If you are still having this problem, please send the trac-all.log file from one of the 4 subjects. a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lorenzo Pini Sent: Friday, May 10, 2019 4:35:50 PM To: freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] units for tracula output

2019-06-02 Thread Yendiki, Anastasia
Hi Jim - Units of diffusivity are mm^2 / sec. a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios Sent: Thursday, May 9, 2019 4:33:27 PM To: Freesurfer support list Subject: [Freesurfer] units for tracula output Exte