Doug-
It's not really a 'problem' per se, I'm just writing analysis scripts and I only want my terminal to display things that I write, like "Registering subject X" instead of flying through the ras-to-vox tables and such. It's just a visual aesthetic display issue for me.
The cat advice works, but when I cat out the reg-feat2anat output, I get an error message that I never noticed before from when it calls tkregister2.
When I run:
% cat | reg-feat2anat --feat $FSL/$S/$F.feat --subject $S > $MAIN/$S/label/$F/reg-feat2anat.log
I get the error:
----------------------------------------------------------------- INFO: could not find /opt/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /opt/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- ----------------------------------------------------------------- INFO: could not find /opt/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /opt/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- ----------------------------------------------------------------- INFO: could not find /opt/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /opt/fsl/etc/standard/avg152T1_brain.mat file -----------------------------------------------------------------
I don't know why it prints it three times (xyz?). Anyhow, even with this error, everything seems to be perfectly fine when I check the registration manually. If I run the command without the cat option, I notice the error is embedded in the output right after the following command is called up (note $Variables are now replaced by subject info):
tkregister2 --targ /opt/fsl/etc/standard/avg152T1_brain.img --mov /labs/tricam/data1/twin/fsl_analysis/BOLD_heritability_analysis/01_00/funcA.feat/example_func.nii.gz --fslreg /labs/tricam/data1/twin/fsl_analysis/BOLD_heritability_analysis/01_00/funcA.feat/reg/example_func2standard.mat --reg /labs/tricam/data1/twin/fsl_analysis/BOLD_heritability_analysis/01_00/funcA.feat/reg/freesurfer/std2exf.register.dat --noedit
My version of FSL does not have the /fsl/etc/standard/avg152T1_brain.mat file. Is this a holdover from files available in a previous FSL version when tkregister2 was written? ($Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $)
More importantly, what information is the .mat file supposed to contain (aside from direction cosine info), and do you know how I might 1) generate this .mat file, 2) get tkregister2 to stop looking for it (within the context of reg-feat2anat!), or 3) get tkregister2 to look for an equivalent file available in FSL 3.3.9?
Many Many Thanks,
Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam
Doug Greve wrote:
No, but why is it a problem? You can always cat the output to /dev/null :).
James Porter wrote:
Howdy-
I didn't see any flags in the help files, but are there some 'hidden' commands I could use to attenuate the verbosity of reg-feat2anat and aseg2feat?
Thanks,
Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam http://www.psych.umn.edu/research/tricam
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