Qustion in parameters settings(old version & new vision)

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Yue Yuan

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Mar 23, 2024, 12:51:42 PMMar 23
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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!

Frank Yeh

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Mar 23, 2024, 1:00:27 PMMar 23
to yuanyu...@gmail.com, DSI Studio
> 1、some parameters (such as scheme_balance, check_btable, csf_calibration; initial_dir, interpolation, seed_plan) are no longer recognized.
>

scheme_balance will be automatically enabled depending on the DWI scheme.
check_btable is still working.
csf_calibration is no longer supported because the updated version
will use nQA (the maximum QA normalized to one).
initial_dir, interpolation, seed_plan all have fixed settings and
cannot be changed in the updated version.

> 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?

Set it to different integer values to get different results.

Best regards,
Frank

Yue Yuan

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Mar 25, 2024, 11:22:56 AMMar 25
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Hi, Frank

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.

Frank Yeh

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Mar 25, 2024, 11:27:34 AMMar 25
to yuanyu...@gmail.com, DSI Studio
Could you post the complete log output?
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Yue Yuan

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Mar 27, 2024, 1:25:14 AMMar 27
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I have inserted the slice alignment to get the .trk file when I performed the fiber trace in the previous step.
Commond:
$pathto_dsistudio/dsi_studio --action=trk --source=$pathto_dti/$subj/data.src.gz.odf.gqi.1.25.fib.gz --fiber_count=1000000 --thread_count=4 --random_seed=1 --step_size=0.625 --turning_angle=60 --smoothing=0 --min_length=10 --max_length=300 --method=0 --ref=$pathto_t1/$subj/mri/aparc+aseg.nii --output=$pathto_dti/$subj/1m0.trk.gz

$pathto_dsistudio/dsi_studio --action=ana --source=$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

the complete log output in ana:
DSI Studio version: Chen"陳" Mar 11 2024
| DSI Studio version: Chen"陳"
| action=ana
| source=/Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/data.src.gz.odf.gqi.1.25.fib.gz
| loop=/Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/data.src.gz.odf.gqi.1.25.fib.gz
|-run ana
| | loading /Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/data.src.gz.odf.gqi.1.25.fib.gz...
| |-open FIB file data.src.gz.odf.gqi.1.25.fib.gz
| | | prepare index file for future accelerated loading
| | | loading fiber and image data
| | |-loading image volumes
| | | |_12 ms
| | | initiating data
| | | default template set to young adult
| | | FIB file loaded
| | |_1.516 s
| | output=/Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/1m0.txt
| | tract=/Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/1m0.trk
| |-loading 1m0.trk
| | |_2.285 s
| | host space (native):
| | -1.88525 0 0 228.115
| | 0 -1.88525 0 228.115
| | 0 0 2.5 0
| | 0 0 0 1
| | tractography space (native):
| | -1 -3.49246e-10 3.72529e-09 123.607
| | -4.07454e-10 -1 1.86265e-09 120.604
| | 3.72529e-09 -1.86265e-09 1 -108.021
| | 0 0 0 1
| | A total of 1000000 tracks loaded
| | a total of 1 tract file(s) loaded
| | merging all tracts into one for post-tract analysis
| |-post-tracking analysis
| | | tip_iteration=0
| | | other_slices=/Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/mri/T1.nii
| | | add slice: /Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/mri/T1.nii
| | |-load slices T1.nii
| | | | add new slices: T1
| | | | dimension: (256,256,256)
| | | | running slice registration...
| | | | iso loaded
| | | | ratio lower than 0.5, downsampling template to 2 mm resolution
| | | | registration started
| | | | translocation: -1.99392 -4.92943 -24.7731
| | | | rotation: -0.16927 0.08409 -0.0158859
| | | | scaling: 1 1 1
| | | | shear: 0 0 0
| | | | registration completed
| | | |_6.946 s
| | | size: (256,256,256)resolution: 1 1 1
| | | srow:
| | | -1 -3.49246e-10 3.72529e-09 123.607
| | | -4.07454e-10 -1 1.86265e-09 120.604
| | | 3.72529e-09 -1.86265e-09 1 -108.021
| | | 0 0 0 1
| | | to_dif:
| | | 0.528494 -0.00839631 -0.0445517 0.221447
| | | 0.000801298 0.522907 -0.0890428 4.98945
| | | 0.0341825 0.0668506 0.39289 -48.3529
| | | 0 0 0 1
| | | connectivity=/Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/mri/aparc+aseg.nii
| | | connectivity_type=end
| | | connectivity_value=count,qa,ncount
| | | connectivity_output=matrix,connectogram,measure
| | | loading /Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/mri/aparc+aseg.nii
| | | reading /Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/mri/aparc+aseg.nii as a NIFTI ROI file
| | |-opening file aparc+aseg
| | | | aparc+aseg loaded as multiple ROI file
| | | | looking for region label file /Users/yuanyue/Documents/Code/ECNUdata/YY_1001_1/mri/aparc+aseg.txt
| | | | using freesurfer labels.
| | | | FIB file dimension: (122,122,50) voxel size: 1.88525 1.88525 2.5
| | | | aparc+aseg dimension: (256,256,256) voxel size: 1 1 1
| | | | aparc+aseg has a different dimension from the FIB file. need transformation or warping.
| | | |_291 ms

| | | 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.
| | |_3.14728 m
| |_3.223 m
|_3.22317 m

Frank Yeh

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Mar 27, 2024, 7:10:21 PMMar 27
to yuanyu...@gmail.com, DSI Studio
DSI Studio is updated to fix this bug.
Please download the new version and see if it works for you.
Thank you for reporting this issue!

Frank
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