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-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@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: >>> >>> 1. 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 >>> >>> 2. 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-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@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 >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> 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/ >>> >>> _______________________________________________ >>> 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. >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> 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/ >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > 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/ > > _______________________________________________ > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 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/ _______________________________________________ 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
