Corrupted conversion to mnic/nifti file format

[sotirisnik]

Hi,

We are testing the minc toolkit 1.9.17 on Ubuntu 16.04 & 18.04. We also executed this command
find <root_of_DICOM_files_directory> -type f | xargs -i dcmconv --write-xfer-little {} {}
in order to convert the .dcm files to Little-Endian-Explicit transfer syntax and we are receiving this error

Restructuring...
gsl: bessel_I0.c:216: ERROR: overflow
Default GSL error handler invoked.
noise_estimate --snr /data/loris/data//assembly/990210/V1/mri/native/loris_990210_V1_t1_001.mnc
SNR is:
gsl: bessel_I0.c:216: ERROR: overflow
Default GSL error handler invoked.
noise_estimate --snr /data/loris/data//assembly/990210/V1/mri/native/loris_990210_V1_t1_002.mnc
SNR is:
gsl: bessel_I0.c:216: ERROR: overflow
Default GSL error handler invoked.
noise_estimate --snr /data/loris/data//assembly/990210/V1/mri/native/loris_990210_V1_t1_003.mnc
SNR is:

[gdevenyi]

Hi,

I'm not clear here what program from minc-toolkit you're reporting a problem with.

The program to convert from dicom to MINC is dcm2mnc. We do not supply "dcmconv" comes from the "dcmtk" package.

[sotirisnik]

This output comes from the execution of https://github.com/aces/Loris-MRI/blob/master/batch_uploads_imageuploader.pl. Loris team suggested that this must be an issue of dcm2mnc. The error "
gsl: bessel_I0.c:216: ERROR: overflow" is not part of your toolkit?

[vfonov]

it is an error from GSL library that is used in noise_estimate, which calculates SNR of a scan.
Without knowing what exactly was fed as input to the noise_estimate , it is impossible to say what causes the error.

[vfonov]

by the way, if you execute noise_estimate with a volume that contains only zeros - you will get the error from GSL about overflow