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)