[Neurodebian-devel] ?Change in .mat file formats for fsl 5.0.8 or some other bug with epi_reg

[VOGRIN Simon J]

Dear Neurodebian-devel,

I recently attempted to run a routine Feat analysis on a set of fMRI data acquired on a 3T Skyra scanner.  There had been no changes to data formats, however after what may have been a recent update (running on Ubuntu 12.04), I discovered that the analysis consistently crashed when generating the transformation matrix such as example_func2highres_init.mat or highres2standard.mat just prior to running the epi_reg command:


did not find file: example_func2highres.mat. Generating transform.

/usr/share/fsl/5.0/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres --fmap=unwarp/FM_UD_fmap --fmapmag=unwarp/FM_UD_fmap_mag --fmapmagbrain=unwarp/FM_UD_fmap_mag_brain --echospacing=0.000325 --pedir=y-
terminate called after throwing an instance of 'NEWMAT::SingularException'


Since the update show the following data format for the example_func2highres.mat was represented as:

0x1.0e44ff173e46p+0  0x1.cd283a1c44249p-5  -0x1.383f7ae3b35ebp-5  -0x1.620c66ec0e2a3p+5
-0x1.0a70bad28adc5p-4  0x1.066b80ba814ffp+0  0x1.6d182aac2cbffp-3  -0x1.2b41149986759p+5
0x1.b147276232db4p-5  -0x1.298475b25c4dcp-3  0x1.2e975d7f1191ap+0  -0x1.2e55f4901ab1ep+6
0x0p+0  0x0p+0  0x0p+0  0x1p+0

rather than earlier 4 x 4 matricies which were standard number formats.

To confirm, I reran a dataset that had successfully been analysed with NO changes to the feat "fsf" file, and again the format of the mat file at the point of the crash was consistent with the structure above which seemed very odd.


Could someone confirm whether this is a known issue or a specific change in data format specification that needs to be more completely implement for an upcoming release.

Thanks in advance for any clarification you may be able to provide,

Regards,

Simon Vogrin | Neuroimaging Scientist | Centre for Clinical Neurosciences & Neurological Research
Room 15 5th Floor Daly Wing | St Vincent’s |  35 Victoria Parade Fitzroy VIC 3065
t: +61 3 9288 3653  |  f: +61 3 9288 3350  |  m: +61 (0)414 698 463

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