How can I change name of saved connevtivity matrix in command line interface

[siyarb...@gmail.com]

Hello,

I am currently trying to create connectivity matrices from a group of patients, by reading in their pre-calculated tt.gz files (full tractography output, obtained by --trk for whole brain tractography, and recognize and cluster commands)

I am trying to write a loop in python, where I create a list of DSI studio cli commands and invoke them with subprocess in linux (mostly inspired from https://github.com/GlennRFox/DSI_Studio Work).

I was able to create a correct set of cli commands, and loop over subject directories, and invoke the correct cli commands with correct --tract and --source names in correct directories, only problem is, when I run the script its stuck over-writing only the first tract in the list of tracts I fed in.

Is there possibly a way to let DSI studio add some pre-defined prefix to the connectivity matrices from command line interface? I am aware of --output and --export options but as far as I know they do not output connectivity matrices.

I have also researched a way to change the output of os.subprocess  before it writes the data to disk, but I havent been able to find a solution.

Thank You Very much for the great software! 

[Fang-Cheng Yeh]

The connectivity matrices will be saved by adding file extension to the tract name assigned by --output

Hope this helps.

Frank

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[siyarb...@gmail.com]

Hello Frank

Thank you very much for your prompt answer. 

I Added --output=(file_name) to my commands, but now the command merges all the tracts in the subdirectory, and outputs file_name.tt.gz file, which inclued all the tracts in it, no connectivity matrices are saved. Am I doing something wrong?

Have a great day!

[Fang-Cheng Yeh]

Could you post the command you used and the log output?

You may try updating DSI Studio to see if it works.

Frank

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[siyarb...@gmail.com]

Hello frank!

Here is the command that my script generates, I do not have any logs as there is no export log option in my script, but I will add that and send it to you too.:

/home/ogrenci/Downloads/dsi-studio/dsi_studio --action=ana --source=116423.src.gz.gqi.1.7.fib.gz --tract=116423.src.gz.gqi.1.7.fib.gzAcoustic_Radiation_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzAnterior_Commissure.tt.gz,116423.src.gz.gqi.1.7.fib.gzArcuate_Fasciculus_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzArcuate_Fasciculus_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNIII_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNIII_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNII_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNII_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNVIII_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNVIII_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNVII_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNVII_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNV_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCNV_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCerebellum_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Frontal_Parahippocampal_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Frontal_Parahippocampal_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Frontal_Parietal_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Frontal_Parietal_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Parahippocampal_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Parahippocampal_Parietal_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Parahippocampal_Parietal_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Parahippocampal_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Rarolfactory_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCingulum_Rarolfactory_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorpus_Callosum_Body.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorpus_Callosum_Forceps_Major.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorpus_Callosum_Forceps_Minor.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorpus_Callosum_Tapetum.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticobulbar_Tract_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticobulbar_Tract_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticopontine_Tract_Frontal_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticopontine_Tract_Frontal_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticopontine_Tract_Occipital_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticopontine_Tract_Occipital_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticopontine_Tract_Parietal_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticopontine_Tract_Parietal_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticospinal_Tract_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticospinal_Tract_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticostriatal_Tract_Anterior_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticostriatal_Tract_Anterior_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticostriatal_Tract_Posterior_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticostriatal_Tract_Posterior_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticostriatal_Tract_Superior_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzCorticostriatal_Tract_Superior_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzDentatorubrothalamic_Tract_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzDentatorubrothalamic_Tract_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzExtreme_Capsule_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzExtreme_Capsule_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzFornix_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzFornix_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzFrontal_Aslant_Tract_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzFrontal_Aslant_Tract_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzInferior_Cerebellar_Peduncle_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzInferior_Cerebellar_Peduncle_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzInferior_Fronto_Occipital_Fasciculus_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzInferior_Fronto_Occipital_Fasciculus_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzInferior_Longitudinal_Fasciculus_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzInferior_Longitudinal_Fasciculus_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzMedial_Lemniscus_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzMedial_Lemniscus_R.tt.gz,116423.src.gz.gqi.1.7.fib.gzMiddle_Cerebellar_Peduncle.tt.gz,116423.src.gz.gqi.1.7.fib.gzMiddle_Longitudinal_Fasciculus_L.tt.gz,116423.src.gz.gqi.1.7.fib.gzMiddle_Longitudinal_Fasciculus_R.tt.gz --connectivity=HCP-MMP --output=Acoustic_Radiation_L.tt.gz --connectivity_value=ncount2 --threads=32 --connectivity_type=end

[Fang-Cheng Yeh]

I would suggest using a loop to generate matrix for each track. It is unlikely to work out with all tracts in one command.

Best regards,

Frank

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[siyarb...@gmail.com]

Hi Frank,

Thank you very much for your answers.

It seems that my scipt was feeding a tract name with .tt.gz extension, and DSI studio omits saving connectogram file. When I changed output name to something with no extension, I was able to get connectogram.txt and connectivity.mat.

I really want to thank you again for the great software. 

I am currently trying to run dsi studio on ubuntu20.04 on a virtual machine by digitalocean, It is a very convenient and easy to manage cloud solution. 

DSI studio is running now, but it is using about 10% CPU and around 15% of ram according to digitalocean dashboard. (even though I set --threads=32).

I thinking about opening different parrallel instances of DSI studio, but I would be glad if there is a smarter way. 

Thank you for your patience...

Regards, 

Şiyar

[Fang-Cheng Yeh]

Could you let me know which step is using only 10% CPU and running slow?

I can check to see if I revise it.

Frank

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