--export=stat flag not working

[Debarun De]

Hello,

  I am currently playing around with the dsi_studio CLI commands to track fibers and to get the data from the fiber in another file. Currently, the code that I am running is: 

dsi_studio.exe --action=trk --source=$PATH\xx.src.gz.gqi.1.7.fib.gz --track_id=Arcuate_Fasciculus_R --seed_count=100000 --tip_iteration=0 --roa=xx:Arcuate_Fasciculus_R  --output=$PATH\xx.tt.gz --export=stat > log.txt

I am able to generate the fibers, but I cannot seem to get the export to produce another text document with the statistic information. I keep getting this message from the log.txt file:

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

I have checked the CLI interface guide and --export seems to be correct, yet it is still not generating the text document.

Any help would be appreciated

Thanks! 

[Frank Yeh]

Could you post the full log.txt output here?

Also, did you use the most updated version of DSI Studio?

Frank

[Debarun De]

Thanks for the quick reply.

Here is the full output of log.txt:

DSI Studio May 15 2021, Fang-Cheng Yeh

source=C:\Users\debar\Documents\dsi_studio_64\dsi_studio_64\100206.src.gz.gqi.1.7.fib.gz

action=trk

loading C:\Users\debar\Documents\dsi_studio_64\dsi_studio_64\100206.src.gz.gqi.1.7.fib.gz...

otsu_threshold=0.6

fa_threshold=0

dt_threshold=0.2

turning_angle=0

step_size=0

smoothing=0

min_length=30

max_length=300

method=0

initial_dir=0

interpolation=0

seed_plan=0

random_seed=0

check_ending=0

tip_iteration=0

seed_count=100000

thread_count=4

roa=1:Arcuate_Fasciculus_R

read region from 1:Arcuate_Fasciculus_R

searching 1 from the atlas pool...

loading 1...

loading atlas 1 from the atlas list.

loading Arcuate_Fasciculus_R from 1 atlas

WARNING: 1 is an empty region file

Consider using --action=atk for automatic fiber tracking

loading C:/Users/debar/Documents/dsi_studio_64/dsi_studio_64/track/HCP1065.tt.gz

warping atlas tracks to subject space

track_id=Arcuate_Fasciculus_R

tolerance=16

set target track: Arcuate_Fasciculus_R

start tracking.

thread_count=4

finished tracking.

191 tracts are generated using 100000 seeds.

0 tracts are removed by pruning.

The final analysis results in 191 tracts.

output=C:\Users\debar\Documents\Batch\1.tt.gz

saving 100206.src.gz.gqi.1.7.fib.gz.tt.gz

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

I am using the May 15 2021 version, that is the most updated version correct?

Thanks!

[Frank Yeh]

Sorry it is not the most updated version.
Could you update the tool again and see if it works?
Frank

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[Debarun De]

Interesting, I tried redownloading the software using the http://dsi-studio.labsolver.org/dsi-studio-download link for windows(the google drive link to be particular), and the version provided is the May 15 2021 version. Am I using the wrong link to download the newest version of dsi-studio?

[Frank Yeh]

Sorry it is my mistake. I committed the update again. It should June
version at the google drive link.
Best regards,
Frank

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[Debarun De]

Thanks for the continued help,

I have downloaded the June version, but now the line of code that I am trying to run from the batch file is crashing after it loads in the custom roa file.

Here is the log.txt output:

DSI Studio Jun  2 2021, Fang-Cheng Yeh

source=C:\Users\debar\Documents\dsi_studio_64\dsi_studio_64\100206.src.gz.gqi.1.7.fib.gz

action=trk

loading C:\Users\debar\Documents\dsi_studio_64\dsi_studio_64\100206.src.gz.gqi.1.7.fib.gz...

otsu_threshold=0.6

fa_threshold=0

dt_threshold=0.2

turning_angle=0

step_size=0

smoothing=0

min_length=30

max_length=300

method=0

initial_dir=0

interpolation=0

seed_plan=0

random_seed=0

check_ending=0

tip_iteration=0

seed_count=100000

thread_count=4

roa=10:Arcuate_Fasciculus_R

read region from 10:Arcuate_Fasciculus_R

searching 10 from the atlas pool...

loading 10...

loading atlas 10 from the atlas list.

running normalization

Here is the code:

dsi_studio.exe --action=trk --source=C:\Users\debar\Documents\dsi_studio_64\dsi_studio_64\100206.src.gz.gqi.1.7.fib.gz --track_id=Arcuate_Fasciculus_R --seed_count=100000 --tip_iteration=0 --roa=10:Arcuate_Fasciculus_R  --output=C:\Users\debar\Documents\Batch\1.tt.gz --export=stat > log.txt

Thanks again,

[Frank Yeh]

You may need to remove the --roa parameter.
Frank

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[Debarun De]

for the june version, is the --roa parameter changed from the may version? I just tested the code without the --roa parameter and it works now but I need to include a region of avoidance for what I am trying to accomplish (within the batch script).

Thanks.

[Frank Yeh]

The ROA parameter will exclude any track that go to the assigned region.
I am not sure the role of adding it here, especially when AF_R is the
tracking target.
Also, the --roa has to assign the atlas name or a NIFTI file name. The
parameters assigned will not work.
Hope this helps.
Frank

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[Debarun De]

I also tried the command without the track_id parameter and with the FreeSurferDKT atlas for an roa and it still did not work, is this an issue with the parameters I inputted?

log.txt output:

DSI Studio Jun  2 2021, Fang-Cheng Yeh

source=C:\Users\debar\Documents\dsi_studio_64\dsi_studio_64\100206.src.gz.gqi.1.7.fib.gz

action=trk

loading C:\Users\debar\Documents\dsi_studio_64\dsi_studio_64\100206.src.gz.gqi.1.7.fib.gz...

otsu_threshold=0.6

fa_threshold=0

dt_threshold=0.2

turning_angle=0

step_size=0

smoothing=0

min_length=30

max_length=300

method=0

initial_dir=0

interpolation=0

seed_plan=0

random_seed=0

check_ending=0

tip_iteration=0

seed_count=100000

thread_count=4

roa=FreeSurferDKT:Arcuate_Fasciculus_R

read region from FreeSurferDKT:Arcuate_Fasciculus_R

searching FreeSurferDKT from the atlas pool...

loading atlas FreeSurferDKT from the atlas list.

running normalization

Code:

dsi_studio.exe --action=trk --source=C:\Users\debar\Documents\dsi_studio_64\dsi_studio_64\100206.src.gz.gqi.1.7.fib.gz --seed_count=100000 --tip_iteration=0 --output=C:\Users\debar\Documents\Batch\1.tt.gz --roa=FreeSurferDKT:Arcuate_Fasciculus_R --export=stat > log.txt

[Frank Yeh]

FreeSurferDKT does not have a region called Arcuate_Fasciculus_R
You may check each atlas's region at [Step T3a][Atlas]
I should fix DSI Studio to report this.
Frank

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[Frank Yeh]

It seems that the pipeline was not finished yet at "running normalization"