--output argumetnt for autotrack

[Steven Jay Granger]

Hi Frank, 

I am working with DSI studio through singularity and using the --action=atk to autotrack a few bundles at once (separated by commas) 

I would like to specify the output directory but it seems that the respective .tt.gz and .txt files are by default written to the current directory. 

I have not been able to specify an --output location for where I would like these directories to be written to (i.e. a subject folder in a different location). 

Am I missing something here by any chance or is there a better way to indicate where the files end up? 

Thanks! 

-Steve 

[Fang-Cheng Yeh]

Hi Steve,

    Sorry for the late reply. I will see if this can be done in future versions.

Best,

Frank

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[Fang-Cheng Yeh]

An update is undergoing at https://github.com/frankyeh/DSI-Studio/actions/runs/3131937093

Once ready, you can use --action=atk --source=*.fib.gz --output=/folder

On Wed, Sep 14, 2022 at 11:32 AM Steven Jay Granger <gran...@uci.edu> wrote:

[Steven Jay Granger]

Thank you for this Frank! 

I was also curious to know if there was a function to specify writing files to trk.gz or tt.gz format for atk? Alternatively, is there a dsi studio command-line function that would readily convert .tt.gz to .trk.gz format? 

[Fang-Cheng Yeh]

I will review code to see if this is possible.
Frank

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/c4f03944-fe8c-44ad-b696-0ee955a4b981n%40googlegroups.com.

[Steven Jay Granger]

Thank you Frank!! 

Fingers crossed that this is possible.

[Fang-Cheng Yeh]

Thanks for the reminder!
It turns out to be a quick revision.
In the updated version, you may assign --trk_format=trk.gz (default is tt.gz)

The build is undergoing at
https://github.com/frankyeh/DSI-Studio/actions/runs/3198259818
Should be ready in an hour.
Frank

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[Fang-Cheng Yeh]

Sorry, there is a glitch caught by the testing process and an update
is currently under build:
https://github.com/frankyeh/DSI-Studio/actions/runs/3200657143

[Steven Jay Granger]

No worries and thank you for creating the update!! 

On Thu, Oct 6, 2022 at 5:44 PM Fang-Cheng Yeh <fran...@gmail.com> wrote:

Sorry, there is a glitch caught by the testing process and an update
is currently under build:

https://urldefense.com/v3/__https://github.com/frankyeh/DSI-Studio/actions/runs/3200657143__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NGOEZG3ttXAyNZepA0g-CDKAhoCu-K24pMo8RK7bTfbbakJNmb_Aab4Cxo-IrFWrDCMDR1ONArqm1hSU$ 

On Thu, Oct 6, 2022 at 11:05 AM Fang-Cheng Yeh <fran...@gmail.com> wrote:
>
> Thanks for the reminder!
> It turns out to be a quick revision.
> In the updated version, you may assign --trk_format=trk.gz (default is tt.gz)
>
> The build is undergoing at

> https://urldefense.com/v3/__https://github.com/frankyeh/DSI-Studio/actions/runs/3198259818__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NGOEZG3ttXAyNZepA0g-CDKAhoCu-K24pMo8RK7bTfbbakJNmb_Aab4Cxo-IrFWrDCMDR1ONArdcxaa_$ 

> Should be ready in an hour.
> Frank
>
> On Thu, Oct 6, 2022 at 10:33 AM Steven Jay Granger <gran...@uci.edu> wrote:
> >
> > Thank you Frank!!
> >
> > Fingers crossed that this is possible.
> >
> >
> > On Friday, September 30, 2022 at 12:00:00 PM UTC-4 Frank Yeh wrote:
> >>
> >> I will review code to see if this is possible.
> >> Frank
> >>
> >> On Fri, Sep 30, 2022 at 9:41 AM Steven Jay Granger <gran...@uci.edu> wrote:
> >> >
> >> > Thank you for this Frank!
> >> >
> >> > I was also curious to know if there was a function to specify writing files to trk.gz or tt.gz format for atk? Alternatively, is there a dsi studio command-line function that would readily convert .tt.gz to .trk.gz format?
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On Monday, September 26, 2022 at 8:04:48 PM UTC-4 Frank Yeh wrote:
> >> >>

> >> >> An update is undergoing at https://urldefense.com/v3/__https://github.com/frankyeh/DSI-Studio/actions/runs/3131937093__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NGOEZG3ttXAyNZepA0g-CDKAhoCu-K24pMo8RK7bTfbbakJNmb_Aab4Cxo-IrFWrDCMDR1ONAnAx8ZEK$ 

> >> >> Once ready, you can use --action=atk --source=*.fib.gz --output=/folder
> >> >>
> >> >> On Wed, Sep 14, 2022 at 11:32 AM Steven Jay Granger <gran...@uci.edu> wrote:
> >> >>>
> >> >>> Hi Frank,
> >> >>>
> >> >>> I am working with DSI studio through singularity and using the --action=atk to autotrack a few bundles at once (separated by commas)
> >> >>>
> >> >>> I would like to specify the output directory but it seems that the respective .tt.gz and .txt files are by default written to the current directory.
> >> >>>
> >> >>> I have not been able to specify an --output location for where I would like these directories to be written to (i.e. a subject folder in a different location).
> >> >>>
> >> >>> Am I missing something here by any chance or is there a better way to indicate where the files end up?
> >> >>>
> >> >>> Thanks!
> >> >>>
> >> >>> -Steve
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>> --
> >> >>> You received this message because you are subscribed to the Google Groups "DSI Studio" group.
> >> >>> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.

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> >> >
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> >
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Steven J. Granger | Graduate Student Researcher

Center for the Neurobiology of Learning and Memory

Department of Neurobiology and Behavior

University of California, Irvine

gran...@uci.edu 

[Steven Jay Granger]

Hi Frank, 

For some reason I am still producing .tt.gz files with the new update and with the addition of --trk_format=trk.gz

Here is the call: 

singularity exec -B /data /data/singularity-images/dsistudio_20221006.sif dsi_studio --action=atk --source=*fib.gz --thread_count=3 --trk_format=trk.gz --output=TEST --track_id=Uncinate,Cingulum,Fornix

Is this an issue with the singularity version perhaps not being updated or does the order of the --trk_format argument matter? 

[Fang-Cheng Yeh]

Could you post the log output?
It will tell whether trk_format is used.
Frank

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAM3kJ8g855CH4EDf4Rmp55hW8ZZAVtA6vyuxuj-y%3DC3avzCQUA%40mail.gmail.com.

[Steven Jay Granger]

Heres the output: 

sh-4.2$ singularity exec -B /data /data/singularity-images/dsistudio_20221006.sif dsi_studio --action=atk --source=*fib.gz --thread_count=3 --trk_format=trk.gz --output=/data/TEST --track_id=Uncinate,Cingulum,Fornix

+ DSI Studio version: Chen"陳" command line

| DSI Studio version: Chen"陳"

| action=atk

| source=*fib.gz

| + run atk

| | searching *fib.gz

| | found 1 files.

| | track_id=Uncinate,Cingulum,Fornix

| | target tracks: Cingulum_Frontal_Parahippocampal_L Cingulum_Frontal_Parahippocampal_R Cingulum_Frontal_Parietal_L Cingulum_Frontal_Parietal_R Cingulum_Parahippocampal_Parietal_L Cingulum_Parahippocampal_Parietal_R Cingulum_Parahippocampal_L Cingulum_Parahippocampal_R Cingulum_Parolfactory_L Cingulum_Parolfactory_R Uncinate_Fasciculus_L Uncinate_Fasciculus_R Fornix_L Fornix_R

| | tolerance=22,26,30

| | track_voxel_ratio=2

| | yield_rate=1e-05

| | tip_iteration=48

| | export_stat=1

| | export_trk=1

| | overwrite=0

| | export_template_trk=0

| | check_ending=1

| | thread_count=3

| | trk_format=trk.gz

| | output=/data/TEST

| | + automatic fiber tracking

| | | + eddy0730_outlierfreedata

| | | | processing eddy0730_outlierfreedata

| | | | + tracking pathways

| | | | | + Cingulum_Frontal_Parahippocampal_L

| | | | | | + open FIB file

| | | | | | | + opening eddy0730_outlierfreedata.icbm152_adult.qsdr.1.3.R67.fib.gz

| | | | | | | |_421 ms

| | | | | | | + loading fiber and image data

| | | | | | | | + loading image volumes

| | | | | | | | |_44 ms

| | | | | | | | + initiating data

| | | | | | | | | matched template: /opt/dsi-studio/atlas/ICBM152_adult/ICBM152_adult.QA.nii.gz

| | | | | | | | |_1 ms

| | | | | | | |_45 ms

| | | | | | | FIB file loaded

| | | | | | |_467 ms

| | | | | | + loading ICBM152_adult.tt.gz

| | | | | | | + opening ICBM152_adult.tt.gz

| | | | | | | |_39 ms

| | | | | | |_60 ms

| | | | | | + opening ICBM152_adult.QA.nii.gz

| | | | | | |_1 ms

| | | | | | + reading image data

| | | | | | |_68 ms

| | | | | | + warping atlas tracks to subject space

| | | | | | |_21 ms

| | | | | | min_length(mm): 88.3862

| | | | | | max_length(mm): 298.679

| | | | | | + tracking Cingulum_Frontal_Parahippocampal_L

| | | | | | | + loading tractography atlas

| | | | | | | convert tolerance distance of 22 from ICBM mm to 14.6667 subject voxels

| | | | | | | creating seed region from tractography atlas

| | | | | | | region dimension: (104,126,90)

| | | | | | | region voxel size: 1.5 1.5 1.5

| | | | | | | region voxel count: 1688

| | | | | | | creating ROA region to limit tracking results

| | | | | | | apply left mask for Cingulum_Frontal_Parahippocampal_L

| | | | | | | yield rate (tract generated per seed): 0.00781569

| | | | | | | tract yield rate (tracts per second): 1126.99

| | | | | | | seed yield rate (seeds per second): 144195

| | | | | | | + save trajectories to eddy0730_outlierfreedata.Cingulum_Frontal_Parahippocampal_L.tt.gz

| | | | | | | | + compressing trajectories

| | | | | | | | |_6 ms

| | | | | | | | + saving file

| | | | | | | | |_57 ms

| | | | | | | |_64 ms

| | | | | | |_18.864 s

| | | | | | + export tracts statistics

| | | | | | | saving /data/TEST/Cingulum_Frontal_Parahippocampal_L/eddy0730_outlierfreedata.Cingulum_Frontal_Parahippocampal_L.stat.txt

| | | | | | | region dimension: (104,126,90)

| | | | | | | region voxel size: 1.5 1.5 1.5

| | | | | | | region voxel count: 70

| | | | | | | region dimension: (104,126,90)

| | | | | | | region voxel size: 1.5 1.5 1.5

| | | | | | | region voxel count: 344

| | | | | | | rdi loaded

| | | | | | | ad loaded

| | | | | | | t1w loaded

| | | | | | | dti_fa loaded

| | | | | | | iso loaded

| | | | | | | md loaded

| | | | | | | rd loaded

| | | | | | | nrdi06L loaded

| | | | | | | nrdi04L loaded

| | | | | | | nrdi02L loaded

| | | | | | |_351 ms

| | | | | |_19.879 s

| | | | | + Cingulum_Frontal_Parahippocampal_R

| | | | | | min_length(mm): 87.374

| | | | | | max_length(mm): 283.229

| | | | | | + tracking Cingulum_Frontal_Parahippocampal_R

| | | | | | | + loading tractography atlas

| | | | | | | convert tolerance distance of 22 from ICBM mm to 14.6667 subject voxels

| | | | | | | creating seed region from tractography atlas

| | | | | | | region dimension: (104,126,90)

| | | | | | | region voxel size: 1.5 1.5 1.5

| | | | | | | region voxel count: 1694

| | | | | | | creating ROA region to limit tracking results

| | | | | | | apply right mask for Cingulum_Frontal_Parahippocampal_R

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[Fang-Cheng Yeh]

Thanks for the help! I found the problem and fixed it:
https://github.com/frankyeh/DSI-Studio/actions/runs/3206100190

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