Yes, it must have been something added by the mail program. I did not see any differences manually (perhaps a new line?), but worked fine when I overwrote the old file with the changes you made in the new one.
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: 07 August 2014 16:41 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bblabel
You have to be in the folder where mri_mergelabels is located to run the tcsh command. Can you look at the first line in that file and see if it matches the first line in the old one? Something might have gotten added by the mail program
On 08/07/2014 11:25 AM, Agoston Mihalik wrote:
I start tcsh automatically when opening the terminal window.
Anyway, typing 'tcsh mri_mergelabels' throws this error to the terminal: mri_mergelabels: No such file or directory.
In addition, I also tried out the previous mri_mergelabels, it does not throw the error: 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 07 August 2014 16:07 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bblabel
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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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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