Another minor bug/user suggestion report.  When I run mri_glmfit-sim, I get output files even when there are no significant clusters but nothing at all when there are no significant voxels within the mask region:

ERROR: initializing hit map
  No voxels were found that met the threshold criteria within the mask.

Apparently mri_glmfit-sim aborts in the latter case but not the former case.  I'm thinking it might be helpful for it to produce output in the former case as well and to have some kind of message in the summary file to the effect that there were no significant voxels, just to be consistent.

Cheers!

Joe

On May 27, 2013, at 9:39 AM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

Hi Joseph,

Thanks for the report. 

-Zeke

On May 25, 2013, at 11:09 PM, Joseph Dien <jdien07@mac.com> wrote:

when I run: isxconcat-sess -sf sessidlist.dat -analysis CPA.sm05.lh -all-contrasts -o secondLevel 

I get the error messages:

secondLevel/CPA.sm05.mni305/log/isxconcat.log

stat: illegal option -- c

usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...]

stat: illegal option -- c

usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...]

stat: illegal option -- c

usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ]

...


I'm assuming this isn't a serious problem as it just seems to affect what goes into the log file but thought you might want to know.
This is on OS X 10.8.2 with Freesurfer 5.2.0.

Cheers!

Joe   

--------------------------------------------------------------------------------

Joseph Dien,
Senior Research Scientist
University of Maryland 

Phone: 301-226-8848
Fax: 301-226-8811











_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


--------------------------------------------------------------------------------

Joseph Dien,
Senior Research Scientist
University of Maryland 

Phone: 301-226-8848
Fax: 301-226-8811