Hi,
I've encountered some issues with parameter settings while using DSI Studio.
In the previous version(Jan 2022), I used the following commands for data reconstruction and fiber tracking:
$pathto_dsistudio/dsi_studio --action=rec --thread=4 --source=$pathto_dti/$subj/data_ecc.src.gz --method=4 --param0=1.25 --scheme_balance=1 --check_btable=1 --csf_calibration=1 --output_rdi=0 --output_dif=0 --mask=$pathto_dti/$subj/nodif_brain_mask.nii.gz
$pathto_dsistudio/dsi_studio --action=trk --source=$pathto_dti/$subj/data_ecc.src.gz.odf8.f5.bal.csfc.012fy.gqi.1.25.fib.gz --fiber_count=1000000 --initial_dir=0 --thread_count=4 --seed_plan=0 --interpolation=0 --random_seed=1 --step_size=0.625 --turning_angle=60 --smoothing=0 --min_length=10 --max_length=300 --method=0 --ref=$pathto_dti/$subj/mri/aparc+aseg.nii --output=$pathto_dti/$subj/1m0.trk.gz
(Randomly select different seed points each time to generate 10 .trk files from 1m0.trk.gz to 1m9.trk.gz)
However, in the new version(May 2024), I found some problems:
1、some parameters (such as scheme_balance, check_btable, csf_calibration; initial_dir, interpolation, seed_plan) are no longer recognized.
2、the definition of random_seed seems to have changed. I am looking to implement a process where each fiber tracking session randomly selects different seed points. Which parameter should I use for this purpose now?
3、I attempted to access the documentation for the previous versions at link(https://sites.google.com/a/labsolver.org/sites/system/errors/WebspaceNotFound?path=%2Fdsi-studio%2F), but the page could not be found.
I would appreciate any guidance on the new parameters that correspond to the old ones and how to adapt to the change in random_seed.
Thank you for your time and assistance!
Thank you very much for your previous answers!
I have another problem. I'm trying to generate a structural connectivity matrix based on the DK brain region segmentation, but I'm getting an error.
The command is as follows:
$pathto_dsistudio/dsi_studio
--action=ana
--source=$pathto_dti/$subj/data.src.gz.odf.gqi.1.25.fib.gz
--tract=$pathto_dti/$subj/1m0.trk
--other_slices=$pathto_t1/$subj/mri/T1.nii
--connectivity=$pathto_t1/$subj/mri/aparc+aseg.nii
--connectivity_value=count,qa,ncount
--connectivity_type=end
--output=$pathto_dti/$subj/1m0.txt
ERROR: No strategy to align aparc+aseg with FIB. If aparc+aseg is in the MNI space, specify mni in the file name (e.g. region_mni.nii.gz). If not, use --other_slices to load the reference T1W/T2W to guide the registration.