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frankyeh / DSI-Studio

A Tractography Tool for Diffusion MRI
http://dsi-studio.labsolver.org
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How can these metrics be extracted to generate nii files? #87

Closed Luoyu-Wang closed 2 months ago

Luoyu-Wang commented 3 months ago

Hi! I have upgraded to the latest version of the software and used the --other_output=all option, but it did not generate any metrics. These images seem to be contained in fib files, how can these metrics be extracted to generate nii files?

frankyeh commented 3 months ago

Could you post the complete command used and the output from the command line during the reconstruction? Frank

On Sat, Apr 6, 2024 at 8:20 AM Luoyu-Wang @.***> wrote:

Hi! I have upgraded to the latest version of the software and used the --other_output=all option, but it did not generate any metrics. What could be the reason? No errors were reported

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Luoyu-Wang commented 3 months ago

Thanks Frank, here is the command line and output: dsistudio --action=rec --source=DwiImgDenDegUEddyPyDesignerSRC/*.src.gz --method=4 --output=ParametersDwiDSIStudioSRCFIB/ --other output=all --thread_count=16 --param0=1.5 --csf_calibration=1

S0001.src.gz.gqi.1.5.fib.gz S0002.src.gz.gqi.1.5.fib.gz ...

frankyeh commented 3 months ago

You may add > log.txt to redirect the console output and post them here. Frank

On Tue, Apr 9, 2024 at 10:28 PM Luoyu-Wang @.***> wrote:

Thanks Frank, here is the command line and output: dsistudio --action=rec --source=DwiImgDenDegUEddyPyDesignerSRC/*.src.gz --method=4 --output=ParametersDwiDSIStudioSRCFIB/ --other output=all --thread_count=16 --param0=1.5 --csf_calibration=1

S0001.src.gz.gqi.1.5.fib.gz S0002.src.gz.gqi.1.5.fib.gz ...

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Luoyu-Wang commented 3 months ago

OK, here is the log.txt DSI Studio version: Chen"陳" Mar 29 2024 | cannot obtain GPU driver and device information (CUDA ERROR 35). please update the Nvidia driver and install CUDA Toolkit. | DSI Studio version: Chen"陳" | action=rec | source=DwiImgDenoiseDegibbsUEddyPyDesignerSRC/.src.gz | loop=DwiImgDenoiseDegibbsUEddyPyDesignerSRC/.src.gz |-processing loop | | a total of 2 files found | | loop_thread=1 | | DwiImgDenoiseDegibbsUEddyPyDesignerSRC/.src.gz->DwiImgDenoiseDegibbsUEddyPyDesignerSRC/S0001.src.gz | | loop= | | action=rec | |-run rec | | | source=DwiImgDenoiseDegibbsUEddyPyDesignerSRC/S0001.src.gz | | |-open SRC file S0001.src.gz | | | | generating mask | | | |_1.117 s | | |-reconstruction parameters | | | | method=4 | | | | odf_resolving=0 | | | | record_odf=0 | | | | dti_no_high_b=1 | | | | other_output=all | | | | r2_weighted=0 | | | | thread_count=16 | | | | param0=1.5 | | | | param1=3000 | | | | param2=0.05 | | | | template 0: "ICBM152_adult.QA.nii" | | | | template 1: "C57BL6_mouse.QA.nii" | | | | template 2: "dHCP_neonate.QA.nii" | | | | template 3: "INDI_rhesus.QA.nii" | | | | template 4: "Pitt_marmoset.QA.nii" | | | | template 5: "WHS_SD_rat.QA.nii" | | | | template=0 | | | |_1 ms | | | motion_correction=0 | | |-additional processing steps | | | | check_btable=0 | | | |_0 ms | | | output=ParametersDwiDSIStudioSRCFIB1/ | | |-initializing | | | | 11ReadDWIData | | | | 10Dwi2Tensor | | | | 13BalanceScheme | | | | 9GQI_Recon | | | | 9RDI_Recon | | | | 11SaveMetrics | | | |_41 ms | | |-GQI | | | |_3.836 s | | |-output | | | | 11ReadDWIData | | | | 10Dwi2Tensor | | | | 13BalanceScheme | | | | 9GQI_Recon | | | | 9RDI_Recon | | | | 11SaveMetrics | | | |_854 ms | | | FIB file saved: ParametersDwiDSIStudioSRCFIB1//S0001.src.gz.gqi.1.5.fib.gz | | |_5.87 s | | DwiImgDenoiseDegibbsUEddyPyDesignerSRC/.src.gz->DwiImgDenoiseDegibbsUEddyPyDesignerSRC/S0002.src.gz | | loop= | | action=rec | |-run rec | | | source=DwiImgDenoiseDegibbsUEddyPyDesignerSRC/S0002.src.gz | | |-open SRC file S0002.src.gz | | | | generating mask | | | |_1.105 s | | |-reconstruction parameters | | | | method=4 | | | | odf_resolving=0 | | | | record_odf=0 | | | | dti_no_high_b=1 | | | | other_output=all | | | | r2_weighted=0 | | | | thread_count=16 | | | | param0=1.5 | | | | param1=3000 | | | | param2=0.05 | | | | template 0: "ICBM152_adult.QA.nii" | | | | template 1: "C57BL6_mouse.QA.nii" | | | | template 2: "dHCP_neonate.QA.nii" | | | | template 3: "INDI_rhesus.QA.nii" | | | | template 4: "Pitt_marmoset.QA.nii" | | | | template 5: "WHS_SD_rat.QA.nii" | | | | template=0 | | | |_2 ms | | | motion_correction=0 | | |-additional processing steps | | | | check_btable=0 | | | |_0 ms | | | output=ParametersDwiDSIStudioSRCFIB1/ | | |-initializing | | | | 11ReadDWIData | | | | 10Dwi2Tensor | | | | 13BalanceScheme | | | | 9GQI_Recon | | | | 9RDI_Recon | | | | 11SaveMetrics | | | |_40 ms | | |-GQI | | | |_3.897 s | | |-output | | | | 11ReadDWIData | | | | 10Dwi2Tensor | | | | 13BalanceScheme | | | | 9GQI_Recon | | | | 9RDI_Recon | | | | 11SaveMetrics | | | |_907 ms | | | FIB file saved: ParametersDwiDSIStudioSRCFIB1//S0002.src.gz.gqi.1.5.fib.gz | | |_5.97 s | |_11.843 s |_11.845 s WARNING: --csf_calibration is not used/recognized. Did you mean --motion_correction ?

frankyeh commented 3 months ago

you may use the following command to export the metrics:

dsi_studio --action=exp --source=*.fib.gz --export=dti_fa,ad,rd

For a list of metrics that can be exported, you may get the names by opening a FIB file at GUI (Step T3).

On Tue, Apr 9, 2024 at 11:12 PM Luoyu-Wang @.***> wrote:

OK, here is the log.txt �[1;34mDSI Studio version: Chen"陳" Mar 29 2024�[0m | cannot obtain GPU driver and device information (CUDA ERROR 35). please update the Nvidia driver and install CUDA Toolkit. | �[0;33mDSI Studio version�[0m: Chen"陳" | �[0;32maction�[0m=rec | �[0;32msource�[0m=DwiImgDenoiseDegibbsUEddyPyDesignerSRC/ .src.gz | �[0;32mloop�[0m=DwiImgDenoiseDegibbsUEddyPyDesignerSRC/.src.gz |-�[1;34mprocessing loop�[0m | | a total of 2 files found | | �[0;32mloop_thread�[0m=1 | | DwiImgDenoiseDegibbsUEddyPyDesignerSRC/

.src.gz->DwiImgDenoiseDegibbsUEddyPyDesignerSRC/S0001.src.gz | | �[0;32mloop�[0m= | | �[0;32maction�[0m=rec | |-�[1;34mrun rec�[0m | | | �[0;32msource�[0m=DwiImgDenoiseDegibbsUEddyPyDesignerSRC/S0001.src.gz | | |-�[1;34mopen SRC file S0001.src.gz�[0m | | | | generating mask | | | |_1.117 s | | |-�[1;34mreconstruction parameters�[0m | | | | �[0;32mmethod�[0m=4 | | | | �[0;32modf_resolving�[0m=0 | | | | �[0;32mrecord_odf�[0m=0 | | | | �[0;32mdti_no_high_b�[0m=1 | | | | �[0;32mother_output�[0m=all | | | | �[0;32mr2_weighted�[0m=0 | | | | �[0;32mthread_count�[0m=16 | | | | �[0;32mparam0�[0m=1.5 | | | | �[0;32mparam1�[0m=3000 | | | | �[0;32mparam2�[0m=0.05 | | | | �[0;33mtemplate 0�[0m: "ICBM152_adult.QA.nii" | | | | �[0;33mtemplate 1�[0m: "C57BL6_mouse.QA.nii" | | | | �[0;33mtemplate 2�[0m: "dHCP_neonate.QA.nii" | | | | �[0;33mtemplate 3�[0m: "INDI_rhesus.QA.nii" | | | | �[0;33mtemplate 4�[0m: "Pitt_marmoset.QA.nii" | | | | �[0;33mtemplate 5�[0m: "WHS_SD_rat.QA.nii" | | | | �[0;32mtemplate�[0m=0 | | | |_1 ms | | | �[0;32mmotion_correction�[0m=0 | | |-�[1;34madditional processing steps�[0m | | | | �[0;32mcheck_btable�[0m=0 | | | |_0 ms | | | �[0;32moutput�[0m=ParametersDwiDSIStudioSRCFIB1/ | | |-�[1;34minitializing�[0m | | | | 11ReadDWIData | | | | 10Dwi2Tensor | | | | 13BalanceScheme | | | | 9GQI_Recon | | | | 9RDI_Recon | | | | 11SaveMetrics | | | |_41 ms | | |-�[1;34mGQI�[0m | | | |_3.836 s | | |-�[1;34moutput�[0m | | | | 11ReadDWIData | | | | 10Dwi2Tensor | | | | 13BalanceScheme | | | | 9GQI_Recon | | | | 9RDI_Recon | | | | 11SaveMetrics | | | |_854 ms | | | �[0;33mFIB file saved�[0m: ParametersDwiDSIStudioSRCFIB1//S0001.src.gz.gqi.1.5.fib.gz | | |_5.87 s | | DwiImgDenoiseDegibbsUEddyPyDesignerSRC/ .src.gz->DwiImgDenoiseDegibbsUEddyPyDesignerSRC/S0002.src.gz | | �[0;32mloop�[0m= | | �[0;32maction�[0m=rec | |-�[1;34mrun rec�[0m | | | �[0;32msource�[0m=DwiImgDenoiseDegibbsUEddyPyDesignerSRC/S0002.src.gz | | |-�[1;34mopen SRC file S0002.src.gz�[0m | | | | generating mask | | | |_1.105 s | | |-�[1;34mreconstruction parameters�[0m | | | | �[0;32mmethod�[0m=4 | | | | �[0;32modf_resolving�[0m=0 | | | | �[0;32mrecord_odf�[0m=0 | | | | �[0;32mdti_no_high_b�[0m=1 | | | | �[0;32mother_output�[0m=all | | | | �[0;32mr2_weighted�[0m=0 | | | | �[0;32mthread_count�[0m=16 | | | | �[0;32mparam0�[0m=1.5 | | | | �[0;32mparam1�[0m=3000 | | | | �[0;32mparam2�[0m=0.05 | | | | �[0;33mtemplate 0�[0m: "ICBM152_adult.QA.nii" | | | | �[0;33mtemplate 1�[0m: "C57BL6_mouse.QA.nii" | | | | �[0;33mtemplate 2�[0m: "dHCP_neonate.QA.nii" | | | | �[0;33mtemplate 3�[0m: "INDI_rhesus.QA.nii" | | | | �[0;33mtemplate 4�[0m: "Pitt_marmoset.QA.nii" | | | | �[0;33mtemplate 5�[0m: "WHS_SD_rat.QA.nii" | | | | �[0;32mtemplate�[0m=0 | | | |_2 ms | | | �[0;32mmotion_correction�[0m=0 | | |-�[1;34madditional processing steps�[0m | | | | �[0;32mcheck_btable�[0m=0 | | | |_0 ms | | | �[0;32moutput�[0m=ParametersDwiDSIStudioSRCFIB1/ | | |-�[1;34minitializing�[0m | | | | 11ReadDWIData | | | | 10Dwi2Tensor | | | | 13BalanceScheme | | | | 9GQI_Recon | | | | 9RDI_Recon | | | | 11SaveMetrics | | | |_40 ms | | |-�[1;34mGQI�[0m | | | |_3.897 s | | |-�[1;34moutput�[0m | | | | 11ReadDWIData | | | | 10Dwi2Tensor | | | | 13BalanceScheme | | | | 9GQI_Recon | | | | 9RDI_Recon | | | | 11SaveMetrics | | | |_907 ms | | | �[0;33mFIB file saved�[0m: ParametersDwiDSIStudioSRCFIB1//S0002.src.gz.gqi.1.5.fib.gz | | |_5.97 s | |_11.843 s |_11.845 s �[1;31mWARNING: --csf_calibration is not used/recognized. Did you mean --motion_correction ?�[0m

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Luoyu-Wang commented 3 months ago

Thank you, Frank, I've got the results based on your advice.. I have a question regarding the FIB file obtained from GQI reconstruction: Are the dti_fa, ad, ra, gfa values based on GQI or are they calculated using DTI?

frankyeh commented 3 months ago

gfa is based on GQI, others are based on DTI.

On Wed, Apr 10, 2024 at 5:00 AM Luoyu-Wang @.***> wrote:

Thank you, Frank, I've got the results based on your advice.. I have a question regarding the FIB file obtained from GQI reconstruction: Are the dti_fa, ad, ra, gfa values based on GQI or are they calculated using DTI?

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Luoyu-Wang commented 3 months ago

Thanks Frank, you solved my problem perfectly!