Try running tcsh mri_mergelabels
On 08/07/2014 05:21 AM, Agoston Mihalik wrote:
Hi Doug
I copied the new script into $FREESURFER_HOME/bin and made it executable, but unfortunately it throws the following error to the Terminal: axm676% mri_mergelabels 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
Best Agoston
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 06 August 2014 23:27 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bblabel
You are correct. The problem is actually that the echo commands sees the question marks and interprets them as wildcards (like *) for file names, but it cannot find such files and it it dies. I've attached a new mri_mergelabels script which should fix the problem. Copy it to $FREESURFER_HOME/bin (you may need to make it executable) doug
On 08/06/2014 08:53 AM, Agoston Mihalik wrote:
I looked more into label files and coordinate systems, and finally I think I found the reasons why bblabel did not work. Here they are:
- The example in bblabel is wrong, because the bounding box points to
the right hemisphere (xmin>0), that's why it returns a file with no vertices (the file contains 2 lines, where the second line is 0), when lh.G_cuneus.label is used as input
- My own label was created with mri_mergelabels and whilst in the original label files the first line looks like this:
#!asciii label , from subject fsaverage vox2ras=TkReg
After merging the first line of the output file looks like this: #label , from subject ??
If I manually edit ?? to fsaverage vox2ras=TkReg, then bblabel works fine also with my label. Otherwise the output file is empty and the terminal output is: Finding points within bounds Writing new label to lh.out.label Echo: No match
Please, could you check if I am right and why mri_mergelabels does not recognise fsaverage and writes out ?? for the first line.
Thanks a lot.
Agoston
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 05 August 2014 23:01 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bblabel
Can you send the full terminal output? Are you sure that there is something in the .label file?
On 08/05/2014 08:47 AM, Agoston Mihalik wrote:
Dear All
I have problems using bblabel and would like to ask for expertise.
At first, I tried to make a coronal cut in the following way:
'bblabel --l lh.DLPFCsd.label --o lh.out.label --ymin 26'
I got a runtime error with:
'echo: No match'
Then I used the example in bblabel help:
'bblabel --l lh.G_cuneus.label --o lh.out.label --xmin 0 --ymax -90 --zmin 10 --zmax 20'
During running it seemed to be fine:
'bblabel done'
However, inspecting the output label in freeview I got the following error:
'no data in label file'
Any help would be appreciated.
Thanks and regards
Agoston
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