Difference between revisions of "Spec2nii"
(Created page with "Category:SoftwareCategory:Converter {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|spec2nii}} |{{#vardefine:url|https://github.com/wexeee/spec2nii}} <!--CONFIGURAT...") |
|||
| (One intermediate revision by one other user not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|spec2nii}} | |{{#vardefine:app|spec2nii}} | ||
| Line 64: | Line 64: | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | Some GE test data comes from the BIG GABA dataset whichw as funded by NIH grant R01 EB016089. Please see Mikkelsen M et al. Big GABA: Edited MR spectroscopy at 24 research sites. NeuroImage 2017;159:32–45. doi: 10.1016/j.neuroimage.2017.07.021 for more information. | |
|}} | |}} | ||
Latest revision as of 13:42, 3 June 2022
Description
A program for multi-format conversion of in vivo MRS to the NIfTI-MRS format.
This program was inspired by the imaging DICOM to NIfTI converter dcm2niix developed by Chris Rorden. All MRS(I) orientations are tested with images converted using dcm2niix. I consider the combination of images converted using dcm2niix and displayed in FSLeyes the de facto standard.
Visualisation of MRS converted by spec2nii can be carried out with a recent (>0.31.0) version of FSLeyes. A FSLeyes plugin for NIfTI-MRS is in development.
Environment Modules
Run module spider spec2nii to find out what environment modules are available for this application.
System Variables
- HPC_SPEC2NII_DIR - installation directory
- HPC_SPEC2NII_BIN - executable directory
Citation
If you publish research that uses spec2nii you have to cite it as follows:
Some GE test data comes from the BIG GABA dataset whichw as funded by NIH grant R01 EB016089. Please see Mikkelsen M et al. Big GABA: Edited MR spectroscopy at 24 research sites. NeuroImage 2017;159:32–45. doi: 10.1016/j.neuroimage.2017.07.021 for more information.