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frankyeh / DSI-Studio

A Tractography Tool for Diffusion MRI
http://dsi-studio.labsolver.org
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DSI-Studio with singularity: --source file does not exist #57

Closed dubergonzoni closed 2 years ago

dubergonzoni commented 3 years ago

Dear Dr Frank Yeah,

I'm trying to run the code below:

singularity exec /usr/local/dsistudio/dsistudio.simg dsi_studio --action=ana --source=/usr/local/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz --tract=/usr/local/Lesion_Quantification/Support_tools/Tractography_Atlas/all_tracts_1mm.trk.gz --output=out_file --connectivity=cfg.parcel_path --connectivity_type=cfg.con_typ --connectivity_threshold=0 --export=tdi

But I'm getting this error:

DSI Studio Mar 20 2021, Fang-Cheng Yeh source=/usr/local/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz action=ana loading /usr/local/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz... /usr/local/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz does not exist. terminating... Warning: --tract is not used. Please check command line syntax. Warning: --output is not used. Please check command line syntax. Warning: --connectivity is not used. Please check command line syntax. Warning: --connectivity_type is not used. Please check command line syntax. Warning: --connectivity_threshold is not used. Please check command line syntax. Warning: --export is not used. Please check command line syntax.

I can't find what I'm doing wrong. Why it's saying the file does not exist it is in the folder? Can you help me, please?

frankyeh commented 3 years ago

Sorry for my late reply. You may try placing HCP842_1mm.fib.gz in another directory to rule out the access problem. Frank

On Sun, Jun 6, 2021 at 12:09 AM Eduardo Bergonzoni Junqueira < @.***> wrote:

Dear Dr Frank Yeah,

I'm trying to run the code below:

singularity exec /usr/local/dsistudio/dsistudio.simg dsi_studio --action=ana --source=/usr/local/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz --tract=/usr/local/Lesion_Quantification/Support_tools/Tractography_Atlas/all_tracts_1mm.trk.gz --output=out_file --connectivity=cfg.parcel_path --connectivity_type=cfg.con_typ --connectivity_threshold=0 --export=tdi

But I'm getting this error:

DSI Studio Mar 20 2021, Fang-Cheng Yeh

source=/usr/local/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz action=ana loading /usr/local/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz... /usr/local/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP842_1mm.fib.gz does not exist. terminating... Warning: --tract is not used. Please check command line syntax. Warning: --output is not used. Please check command line syntax. Warning: --connectivity is not used. Please check command line syntax. Warning: --connectivity_type is not used. Please check command line syntax. Warning: --connectivity_threshold is not used. Please check command line syntax. Warning: --export is not used. Please check command line syntax.

I can't find what I'm doing wrong. Why it's saying the file does not exist it is in the folder? Can you help me, please?

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