neurolabusc
commented
2 years ago @wtclarke can you try out the macOS build here which will report v1.2.20211007 (or if you prefer Linux/Windows tell me). This should convert the complex value to the absolute.
- When a user opens up complex data in FSLeyes, choosing the
Time seriesoption from theViewmenu shows therealcomponent, rather than theabsolute. It is easy to show either, but it might be nice to be consistent across tools. Do you have any preference between these two? - I do think most users will be better served with your MRSView FSLeyes plugin. Both tools are free and open source, so users should choose the best tool for the job. It is easy for a developer to add features, but the user interface starts to become very daunting. My sense is that while MRIcroGL and FSLeyes overlap in basic functionality, they serve different niches and overall they complement each other rather than compete.
- Your exemplar datatype is in
DT_COMPLEX128. Do any of your tools generateDT_COMPLEX64orDT_COMPLEX256? If so, can you provide examples. Usually I can create different datatypes with fslmaths using the-odtoption, but the current version of fslmaths does not support complex data types.
This may reflect the fact that I am using a ARM-based CPU, but I was not able to install the fsleyes-plugin-mrs, and the fmrib gitlab site does not allow outsiders to post issues.
$sysctl -n hw.model
MacBookAir10,1
$ sw_vers
ProductName: macOS
ProductVersion: 11.5.2
BuildVersion: 20G95
$ conda install -c conda-forge fsleyes-plugin-mrs
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): | WARNING conda.models.version:get_matcher(537): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
WARNING conda.models.version:get_matcher(537): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.6.*, but conda is ignoring the .* and treating it as 3.6
WARNING conda.models.version:get_matcher(537): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.*, but conda is ignoring the .* and treating it as 1
done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
wtclarke
pauldmccarthy
Dear Chris,
Would it be possible to include better handling for complex data types in MRIcroGL?
Recently someone reported that MRIcro couldn't load NIfTI-MRS formatted data (created by spec2nii), see spec2nii issue #23. From testing I believe that this arises from MRS data being complex. MRIcroGL reports 'unable to load "my_complex_data.nii.gz"', but will load the same file when the data is non-complex.
Your handling of a 4th time dimension means that (somewhat) meaningful viewing of MRS data can almost be handled. Would you consider loading and simply taking the absolute or real part of the data?
I've attached two very simple files that I tested with. These have 1x1x1x100 random real/complex float data, and in addition a header extension such as NIfTI-MRS uses. n2_float_4dim_hdr.nii.gz n2_cfloat_4dim_hdr.nii.gz