Ironsmith QSM v1.3 Beta
Updates:
- Fixed bug related to #3 .
- Ironsmith will now automatically align all FreeSurfer derived QSM reference masks to the QSM data inside Matlab. This issue occurs because MEDI Toolbox loads the QSM data in Matlab in a slightly different format than the Matlab function niftiread().
- FreeSurfer derived QSM reference mask erosion is now selected based on provided QSM data.
- For instance, less erosion might be used for younger participants who have smaller ventricles whereas more erosion might be used for older adults who might have larger ventricles. This update ensures "too much erosion" does not take place and QSM reference masks always have enough voxels. If without eroding, less than 100 voxels per QSM reference mask are present, Ironsmith will exit with an error describing the issue.
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MEDI Toolbox/Matlab output is now displayed on screen while Ironsmith is running, as with other code. MEDI Toolbox/Matlab output is also saved in the appropriate log file under OutputFolder/Subj/LogFiles.
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Updates to README.md and README.pdf for clarity/readability.
NOTE for Siemens XA30 software users:
MEDI Toolbox (version 01/15/2020) does not support XA30 enhanced DICOMs. To fix this issue:
DICOMs must be exported as "Interoperability" from the MRI scanner console.
A single line of code needs to be changed in one of the MEDI Toolbox (version 01/15/2020) functions:
In file Read_DICOM.m under MEDI_toolbox/functions
Change line 50 from case {'siemens','siemens healthcare gmbh'} to case {'siemens','siemens healthcare gmbh','siemens healthineers'}
NOTE:
Due to the FreeSurfer update, the per-ROI QSM values are not identical between Ironsmith v1.0 and later versions.
Correlation of QSM values extracted from the 89 ROIs offered by Ironsmith, between v1.0 and v1.2, yielded an r^2 value of 0.99.
For this reason, we do not recommend updating Ironsmith mid-analyses. All data should be analyzed with either v1.0 OR v1.2 (FreeSurfer 6.0.0 or FreeSurfer 7.1.1).