Ss3t_csd_beta1 not responding

Hi MRtrix Experts,

I tried using ss3t_csd_beta1 out for b0+single shell but unfortunately ended up with Error (see below please).

I followed the basic pipeline here to calculate FODs map from ex vivo human spinal cord. here is the link for the pipeline I followed https://3tissue.github.io/doc/single-subject.html.

Any help or suggestion is highly appreciated.

Best,

Ibrahim
s4333238@cai-wks1:/30days/s4333238/new_test_fod_dh$ dwi2response dhollander dwi_denoised_unringed_unbiased.mif -mask dwi_mask.mif response_wm.txt response_gm.txt response_csf.txt -grad gradient_4219_1500_18dir.txt
dwi2response:
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
dwi2response:
dwi2response: Generated scratch directory: /30days/s4333238/new_test_fod_dh/dwi2response-tmp-AP5KJL/
dwi2response: Importing DWI data (/30days/s4333238/new_test_fod_dh/dwi_denoised_unringed_unbiased.mif)…
dwi2response: Importing mask (/30days/s4333238/new_test_fod_dh/dwi_mask.mif)…
dwi2response: Changing to scratch directory (/30days/s4333238/new_test_fod_dh/dwi2response-tmp-AP5KJL/)
dwi2response: -------
dwi2response: 2 unique b-value(s) detected: 0,1500 with 2,18 volumes
dwi2response: -------
dwi2response: Preparation:
dwi2response: * Eroding brain mask by 3 pass(es)…
dwi2response: [ mask: 1890787 -> 1542249 ]
dwi2response: * Computing signal decay metric (SDM):
dwi2response: * b=0…
dwi2response: * b=1500…
dwi2response: * Removing erroneous voxels from mask and correcting SDM…
dwi2response: [ mask: 1542249 -> 1542249 ]
dwi2response: -------
dwi2response: Crude segmentation:
dwi2response: * Crude WM versus GM-CSF separation (at FA=0.2)…
dwi2response: [ 1542249 -> 1338350 (WM) & 203899 (GM-CSF) ]
dwi2response: * Crude GM versus CSF separation…
dwi2response: [ 203899 -> 180085 (GM) & 23814 (CSF) ]
dwi2response: -------
dwi2response: Refined segmentation:
dwi2response: * Refining WM…
dwi2response: [ WM: 1338350 -> 1234346 ]
dwi2response: * Refining GM…
dwi2response: [ GM: 180085 -> 114929 ]
dwi2response: * Refining CSF…
dwi2response: [ CSF: 23814 -> 5689 ]
dwi2response: -------
dwi2response: Final voxel selection and response function estimation:
dwi2response: * CSF:
dwi2response: * Selecting final voxels (10.0% of refined CSF)…
dwi2response: [ CSF: 5689 -> 569 ]
dwi2response: * Estimating response function…
dwi2response: * GM:
dwi2response: * Selecting final voxels (2.0% of refined GM)…
dwi2response: [ GM: 114929 -> 2299 ]
dwi2response: * Estimating response function…
dwi2response: * single-fibre WM:
dwi2response: * Selecting final voxels (0.5% of refined WM)…
dwi2response: [ WM: 1234346 -> 6172 (single-fibre) ]
dwi2response: * Estimating response function…
dwi2response: -------
dwi2response: Generating outputs…
dwi2response: -------
dwi2response: Changing back to original directory (/30days/s4333238/new_test_fod_dh)
dwi2response: Deleting scratch directory (/30days/s4333238/new_test_fod_dh/dwi2response-tmp-AP5KJL/)

s4333238@cai-wks1:/30days/s4333238/new_test_fod_dh$ ss3t_csd_beta1 dwi_denoised_unringed_unbiased.mif response_wm.txt wmfod.mif response_gm.txt gm.mif response_csf.txt csf.mif -mask dwi_mask.mif
ss3t_csd_beta1:
ss3t_csd_beta1: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
ss3t_csd_beta1:
ss3t_csd_beta1: -------
mrinfo: [ERROR] no diffusion encoding information found in image “/30days/s4333238/new_test_fod_dh/dwi_denoised_unringed_unbiased.mif”
mrinfo: [ERROR] no diffusion encoding information found in image “/30days/s4333238/new_test_fod_dh/dwi_denoised_unringed_unbiased.mif”
ss3t_csd_beta1: 0 unique b-value(s) detected: with volumes

ss3t_csd_beta1: [ERROR] Need b=0 data and a single non b=0 shell.
s4333238@cai-wks1:/30days/s4333238/new_test_fod_dh$ ss3t_csd_beta1 dwi_denoised_unringed_unbiased.mif response_wm.txt wmfod.mif response_gm.txt gm.mif response_csf.txt csf.mif -mask dwi_mask.mif
ss3t_csd_beta1:
ss3t_csd_beta1: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
ss3t_csd_beta1:
ss3t_csd_beta1: -------
mrinfo: [ERROR] no diffusion encoding information found in image “/30days/s4333238/new_test_fod_dh/dwi_denoised_unringed_unbiased.mif”
mrinfo: [ERROR] no diffusion encoding information found in image “/30days/s4333238/new_test_fod_dh/dwi_denoised_unringed_unbiased.mif”
ss3t_csd_beta1: 0 unique b-value(s) detected: with volumes

ss3t_csd_beta1: [ERROR] Need b=0 data and a single non b=0 shell.
s4333238@cai-wks1:/30days/s4333238/new_test_fod_dh$ ss3t_csd_beta1 dwi_denoised_unringed_unbiased.mif response_wm.txt wmfod.mif response_gm.txt gm.mif response_csf.txt csf.mif -mask dwi_mask.mif -grad gradient_4219_1500_18dir.txt

Error: unrecognized arguments: -grad gradient_4219_1500_18dir.txt
Usage: ss3t_csd_beta1 in_dMRI_data in_SFWM_resp out_WM_FOD in_GM_resp out_GM in_CSF_resp out_CSF [ options ]
(Run ss3t_csd_beta1 -help for more information)

HI Ibrahim,

Unfortunately, we don’t provide support for this version, as outlined in this post. You’ll have better luck submitting an issue directly to the maintainer of that project in the appropriate forum.

Of course, if you come across issues that you can then replicate using the release version of MRtrix, feel free to post here again, and we’ll do what we can to help.

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Hi Ibrahim,

No worries. I replied elsewhere so you’re not stuck. It was because your gradient table wasn’t stored in the header of your (preprocessed) DWI dataset. Regardless, it’s a good idea generally to do this at the start of your pipeline, when importing data. In that way, you can make less mistakes down the track, but also don’t have to constantly provide the gradient table “manually”. I hope that helps.

Cheers,
Thijs

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Hi Dhollander,

I really appreciate your prompt reply. Many thanks! yes exactly that was the problem. I did the steps you suggested and now is working fine.

Many thanks once again.

Cheers,

Ibrahim

1 Like