what do you mean it does not work? Because things aren't aligned? I'm afraid you're on your own if you want the columns to be lined up. I'd suggest a perl script.
doug
Fornito, Alexander wrote:
-b doesn't seem to work. The command is below, and the format of the output, are below. Is this a bug?
mris_anatomical_stats -l 1000027_lh_roi.label -b -log roi.log 1000027 lh white
Output: % 1000027: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 592393 124 321 2.582 0.698 0.068 0.022 4.448 0.588
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sat 9/17/2005 10:33 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] anatomical stats try -b
On Sat, 17 Sep 2005, Fornito, Alexander wrote:
I can create a log file, but in the output, the numbers are out of alignment, so you can't easily figure out what each number refers to. Is there some preferable output format or suffix that I can add to the log file name to adjust this?
Also, I can't seem to use the -f flag to create a table. mris_anatomical_stats runs, but there is no table file output at the end. Is this only for the annotation table (I'm using custom labels)? An example command I've tried is:
mris_anatomical_stats -mgz -l roi.label -f roi_table 1000001 lh white
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 9/16/2005 9:51 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] anatomical stats p.s. the flags should always come before the mandatory command line args.
On Fri, 16 Sep 2005, Fornito, Alexander wrote:
Hi, I'm using the 20050905 distribution and it seems like mris_anatomical_stats is trying to look for cor files, when I've run my analyses using mgz. Is there a way to change this, or have I got it wrong?. Here is the output
mris_anatomical_stats 1000001 lh white reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm... corRead(): can't open file /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm/COR-.info mris_anatomical_stats: could not read input volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/w
Also, I've been having trouble using the -f and -log options (the program runs, but I can't seem to create an output file) with some other surfaces (that I have used cor with). Could you pls give me an example of how to use these flags in the command line? I tried: mris_anatomical_stats 1000027 lh white -l 1000027/label/1000027_roi.label -f roi_stats.log (and I also tried putting the options right after mris_anatomical_stats). Thanks, Alex
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