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Hello, I was able to run amico fully through for my first subject using the following commands...
```
#!/bin/tcsh
#SBATCH --time=300:00:00
#SBATCH --mem=60000
#SBATCH --output=result
#SBATCH -…
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Hi again Robbert,
Many thanks for your help with the set up of MDT on my cluster some time ago. I have been obtaining some promising findings from the ODI maps and now I wish to study the free wate…
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In the new `qsm_sb` model, presence of the outputs depends on the selected options. For example:
```
% Case - Split-Bregman:
% i) W/ magnitude weighting: chiSBM, chiL2M, chiL2, unwrapp…
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We are running mdt-model-fit:
```
mdt-model-fit \
--cl-device-ind 0 -o "output1/powell_double" \
-n "1" \
--double\
--no-recalculate\
"NODDI" \
"data.nii" \
"bvecs.prtcl" \
…
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**Submitting author:** @agahkarakuzu (Agah Karakuzu)
**Repository:** https://github.com/qMRLab/qMRLab
**Version:** v.2.4.1
**Editor:** @Kevin-Mattheus-Moerman
**Reviewer:** @grlee77, @mfroeling, @6244…
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If I'm correct harmonization.py can be used also for multi-shell acquisition (i.e. NODDI). Do I need to specify any value in the --bvalMap for multi-shell data?
Thanks
Fede
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Hi @TinasheMTapera ,
I have solidified the heuristic that auto-populates keys per our goal.
It looks like there's a variable in the code `convert_to_bids` that doesn't recognize `items` within …
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Our original goal was to have users prepare the data before qMRLab and only provide the quantitative fitting. However, as we move to BIDS compatibility #206, and being able to input data directly from…
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Hi,
I have asked about this issue before (https://github.com/daducci/AMICO/issues/56#issuecomment-408090238), but thought I would open a new thread since it is stopping all AMICO analysis at our ne…
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Hello,
My amico program is seeming to report strange final results when processing my NODDI DTI data. Initially, before processing, I had the same issue here:
https://github.com/daducci/AMICO/iss…