I am having difficulties using AimsSNR command line.
As far as I understand, I guess that one has to provide a ROI in which the standard deviation of the noise will be estimated.
It seems that this ROI can be provided either as a sphere (coordinates x,y,z and radius) or as a binary volume. But I can't make any of these options work :
AimsSNR is one of these very old commands that were created before anyone here was born and untouched since then
It uses some obsolete code (e.g. for argument parsing) and does not include the appropriate try/catch structure to display a human readable error message instead of "Abort".
Yes, NmrSNR is in my package and this is exactly what I need. Thanks!
Just two last questions/remarks:
1) When giving the ROI as a mask, I guess that the mean of the signal is computed on the mask and the SD of the noise is computed on the complementary of the mask.
Is it possible to compute the signal and the noise on two different masks which are not complementary sets?
2) The 'NmrSNR' command line works fine except when a ".ima.minf" file is present in the directory.
For example :
For the moment, when specifying a mask with -m option, noise is processed
in the complementary of the given mask.
I understand your requirement and it will be taken into account in the next
release.
As for the crash with a *.ima.minf. In fact, in AIMS the type of items is given
in 'data_type' syntactic argument, whereas in NMR the item type is given in
'item_type' syntactic argument.
Furthermore, in AIMS, item type names are U8, S8, U16, S16, ...
where as in NMR, item type names are uint8_t, int8_t, uint16_t, int16_t, ...
So NmrSNR is crashing because it could not find 'item_type' syntactic
argument.
I will delete the .minf files before calling NmrSNR.
Just out of curiosity, is there a tool that would automatically convert an AIMS-readable ".minf" to a NMR-readable one?