This is not actually an error, just a warning that it cannot find the .mat file. The .mat file is not part of the analyze spec but was something created by SPM to hold direction cosine info, and we have since adopted it. If the .mat file is not there, then freesurfer will make certain assumptions about the DCs. These assumptions are correct for the mni152 volumes in the FSL standard dir.

doug

James N. Porter wrote:

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

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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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