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While I have written a lot of text in various locations regarding core decisions that need to be made regarding the definitions of filesystem paths for DWI derivatives, they may be too verbose or DWI-…
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Dear experts,
My DWI data (data.nii.gz) has no a b0 volume, however, the data has a volume with bvalue=5.
When checking the "bvals" file, I found all b values as follows.
5 5 1490 2995 1495 3005 …
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Tractoflow pipeline does not support multi-shell multi-tissue CSD (MSMT-CSD). Only single shell single tissue (SSST-CSD) has been implemented even though `scil_compute_msmt_fodf.py` and `scil_compute_…
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Hello, I had an error regarding the bval and bvecs files being incorrect or incompatible. I have a feeling it is the arrangement of the bvecs since I had to extract and build them from an .XML file. T…
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Hello!
I have the following DTI scheme:
```
-> Loading data:
* DWI signal
- dim = 108 x 129 x 109 x 96
- pixdim = 1.800 x 1.800 x 1.800
* Acquisition scheme
- 96 samples, 2 shel…
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Hello Dr. Daducci,
This is not an issue but general question in regard to histograms for the AMICO maps that are generated. There are spikes showing up at certain intervals for FICVF and OD histogr…
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Hello,
I am not getting similar results when I fit the same images with AMICO and the NODDItoolbox. While I understand that they are intrinsically different, are there specific parameters that I s…
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Hello,
I am running MDT out of a Singularity container and am getting a runtime error when running the `mdt-model-fit` command. Is there anyway to figure out what the problem is?
```
Singularit…
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Create a file $HOME.bash_aliases in which the bash aliases live
E.g.
```bash
#!/bin/bash
# File for setting aliases
alias KPUM_NODDI='
studydir=/mnt/s/Research/Projects/KPUM_NODDI/Data;
c…
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MRTrix3's `dwibiascorrect` is not working for some reason.
https://github.com/finnlennartsson/kpum_noddi/blob/ec484fee2195be9acda297161d790a0f63a3db6a/shell/dmri_preprocess.sh#L355-L370