How to export .trk file and tract analysis statistics at the same time?

[William Drew]

Hello, 

I am trying to run this command on MacOS

/Applications/dsi_studio.app/Contents/MacOS/dsi_studio --action=ana --source=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz --tract=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/All_Tracts/FPT_L.trk.gz --roi=/Users/williamdrew/Downloads/sub-subh001_lesion.nii.gz --output=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Tract_Disconnection/FPT_L.trk.gz --export=stat

To export a .trk file of the fibers that pass through an ROI and also tract statistics, however, I am getting the message: 

Warning: --export is not used. Please check command line syntax.

Is there something wrong with my command syntax?

Thanks, WD

[Frank Yeh]

Could you post the full message output?

Frank

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[William Drew]

DSI Studio Aug 30 2021, Fang-Cheng Yeh

source=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz

action=ana

loading /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz...

roi=/Users/williamdrew/Downloads/sub-subh001_lesion.nii.gz

read region from /Users/williamdrew/Downloads/sub-subh001_lesion.nii.gz

DWI dimension=(157,189,136)

NIFTI dimension=(182,218,182)

nifti loaded as single ROI file

NIFTI file has a different dimension from DWI.

loaded NIFTI file used as MNI space image.

tract=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/All_Tracts/FPT_L.trk.gz

output=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Tract_Disconnection/FPT_L.trk.gz

loading FPT_L.trk.gz

filtering tracts using roi/roa/end regions.

save all tracts to /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Tract_Disconnection/FPT_L.trk.gz

saving FPT_L.trk.gz

file saved at /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Tract_Disconnection/FPT_L.trk.gz

Warning: --export is not used. Please check command line syntax.

[Frank Yeh]

This issue was recently fixed.

You may update DSI Studio and test it again.

Sorry for the hassle.

Frank

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[William Drew]

With the Nov 16 update, I now have new problems. 

First, DSI_studio is now sometimes crashing (see crash report and screenshot).

Additionally, I am also getting an error "invalid export option:tdi": 

when I run the command 

/Applications/dsi_studio.app/Contents/MacOS/dsi_studio --action=ana --source=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz --tract=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/all_tracts_1mm.trk.gz --roi=/Users/williamdrew/Downloads/sub-subh001_lesion.nii.gz --output=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Parcel_Disconnection/subh001_test.trk.gz --connectivity=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Parcellations/Schaefer_Yeo/Plus_Subcort/Schaefer2018_100Parcels_7Networks_order_plus_subcort.nii --connectivity_type=end --connectivity_threshold=0 --export=tdi

The output is 

DSI Studio Nov 16 2021 Fang-Cheng Yeh

source=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz

action=ana

loading /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz...

output=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Parcel_Disconnection/subh001_test.trk.gz

roi=/Users/williamdrew/Downloads/sub-subh001_lesion.nii.gz

read region from file:/Users/williamdrew/Downloads/sub-subh001_lesion.nii.gz

DWI dimension=(157,189,136)

NIFTI dimension=(182,218,182)

nifti loaded as single ROI file

NIFTI file has a different dimension from DWI.

loaded NIFTI file used as MNI space image.

tract=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/all_tracts_1mm.trk.gz

loading all_tracts_1mm.trk.gz

A total of 138445 tracks loaded

filtering tracts using roi/roa/end regions.

remaining tract count:8215

a total of 1 tract file(s) loaded

saving subh001_test.trk.gz

connectivity=/Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Parcellations/Schaefer_Yeo/Plus_Subcort/Schaefer2018_100Parcels_7Networks_order_plus_subcort.nii

connectivity_type=end

connectivity_value=count

loading /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Parcellations/Schaefer_Yeo/Plus_Subcort/Schaefer2018_100Parcels_7Networks_order_plus_subcort.nii

reading /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Support_Tools/Parcellations/Schaefer_Yeo/Plus_Subcort/Schaefer2018_100Parcels_7Networks_order_plus_subcort.nii as a NIFTI regioin file

DWI dimension=(157,189,136)

NIFTI dimension=(182,218,182)

nifti loaded as multiple ROI file

looking for region label file

using freesurfer labels.

NIFTI file has a different dimension from DWI.

loaded NIFTI file used as MNI space image.

a total of 135 regions are loaded.

connectivity_threshold=0

count tracks by ending

calculate matrix using count

export connectivity matrix to /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Parcel_Disconnection/subh001_test.trk.gz.Schaefer2018_100Parcels_7Networks_order_plus_subcort.count.end.connectivity.mat

export connectogram to /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Parcel_Disconnection/subh001_test.trk.gz.Schaefer2018_100Parcels_7Networks_order_plus_subcort.count.end.connectogram.txt

export network measures to /Users/williamdrew/projects/nimlab/Lesion_Quantification_Toolkit/Outputs/subh001/Parcel_Disconnection/subh001_test.trk.gz.Schaefer2018_100Parcels_7Networks_order_plus_subcort.count.end.network_measures.txt

export=tdi

invalid export option:tdi

[Frank Yeh]

I am sorry about the bug.

I fixed it (hopefully) and a new release is building. You may see the progress here: https://github.com/frankyeh/DSI-Studio/actions

They should be ready in 10~20 minutes, depending on the OS version. 

Once done, you can download new versions to see if it works.

If there are additional issues, please let me know.

Best regards,

Frank

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