Hello,
Upgrades to the underlying C/C++ runtime libraries have generally the cause of some older ( pre 5.0.9 ) FSL binaries outputting hex-files. Updating the version of FSL to 5.0.9 or greater should fix this ( or you could potentially look into if any compiler/library updates have been made on your platform recently ).
Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 8 Dec 2017, at 16:53, Christina Fales <[log in to unmask]> wrote:
>
> Hi FSL Gurus:
>
> Recently I have been running some HCP pipeline scripts (PreFreeSurferPipeline.sh) that I have run successfully many times before. However this time the jobs abort, apparently because the mat files created by robustfov (or possibly aff2rigid) are hexidecimal and not readable by npyio.py's loadtxt routine. I see on the listserv that other users (back in 2015) had related problems, during which Paul McCarthy wrote that this was a known bug that would be fixed. And it must have been fixed because all the subjects I ran 3 months ago ran fine. However, now my new subjects fail, as does one of the older ones which previously ran successfully.
>
> Paul provided a small script for converting from hex back to float, which I could use, but it is likely to be messy and shouldn't be necessary. Also I'm concerned that I don't know the reason why our installation appears to have changed.
>
> All jobs were run using FSL 5.06 (Centos5_64) and the pipeline version is 3.4. We are not aware of having updated any part of the code that is currently failing. The python version is 2.7, and we appear to have version 2.0a0 for gradunwarp, in case that matters.
>
> Would you have any insights on this? The abort messages are below.
>
> Thanks very much,
> Christina Fales
> Psychiatry Research
> Northwell Health
> Glen Oaks, NY 11004
>
> gradunwarp-INFO: Parsing /nethome/amiklos/public_html/myscript/virtualbrain/Pipeline/OurHcpPipeline/coeff.grad for harmonics coeffs
> gradunwarp-INFO: Evaluating spherical harmonics
> gradunwarp-INFO: on a 60^3 grid
> gradunwarp-INFO: with extents -300.0mm to 300.0mm
> gradunwarp-INFO: along x...
> gradunwarp-INFO: along y...
> gradunwarp-INFO: along z...
> gradunwarp-INFO: Evaluating the jacobian multiplier
> gradunwarp-INFO: Unwarping slice by slice
> gradunwarp-INFO: Writing output to trilinear.nii.gz
> Traceback (most recent call last):
> File "/usr/local/opt/fsl-5.0.6-centos5_64/bin/aff2rigid", line 89, in <module>
> a=loadtxt(argv[1])
> File "/usr/lib64/python2.7/site-packages/numpy/lib/npyio.py", line 841, in loadtxt
> items = [conv(val) for (conv, val) in zip(converters, vals)]
> ValueError: invalid literal for float(): 0x1.069c00511611ap+0
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