Command line for slices

[mudat...@gmail.com]

Hi Dr. Frank,

Is there a command line options for marking a slice (e.g., T1w) with roi or tract and export and saving it? I have added an image in the tractography (--action=trk) process using --t1t2=*.nii.gz. I want to export and save the marked same image on a batch of data if available.

Thanks

Mudathir

[Frank Yeh]

Not yet but I am listing this on my to-do list.

I will let you know once available.

Frank

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[mudat...@gmail.com]

Thanks Dr. Frank. Appreciate your hard work. I will wait for your notifications.

Mudathir

[mudat...@gmail.com]

sorry I forgot another question. After I finished the --action=trk process with a --fiber_count=3000000, when I upload the tt.gz file to the dsi studio gui, the number of tracts in the T3d windows is far less than what was constructed. Is this normal for the gui? Example is below

Running whole brain tractography for 105115

DSI Studio Jun 21 2021, Fang-Cheng Yeh

source=/Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/T1w/DWI/*.fib.gz

action=trk

searching *.fib.gz in directory /Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/T1w/DWI

found 1 files.

Process file:/Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/T1w/DWI/data.src.gz.odf8.f5rec.bal.csfc.012fy.rdi.gqi.1.25.fib.gz

source=/Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/T1w/DWI/data.src.gz.odf8.f5rec.bal.csfc.012fy.rdi.gqi.1.25.fib.gz

loading /Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/T1w/DWI/data.src.gz.odf8.f5rec.bal.csfc.012fy.rdi.gqi.1.25.fib.gz...

otsu_threshold=0.6

fa_threshold=0

dt_threshold=0.2

turning_angle=45

step_size=0.16

smoothing=0

min_length=40

max_length=300

method=1

initial_dir=0

interpolation=0

seed_plan=0

random_seed=0

check_ending=0

tip_iteration=0

fiber_count=3000000

seed_count=0

thread_count=10

roa=/Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/dsi/roi/roa.nii.gz

read region from /Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/dsi/roi/roa.nii.gz

t1t2=/Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/T1w/T1w_acpc_dc_restore_brain.nii.gz

registeration complete

1.63713e-19 4.59163e-41 0 0

4.34403e-44 0 -1.04457e-17 4.5772e-41

4.34403e-44 0 3.36312e-43 0

T1T2 dimension: (260,311,260)

T1T2 voxel size: 0.7 0.7 0.7 

DWI dimension=(182,217,182)

NIFTI dimension=(260,311,260)

nifti loaded as single ROI file

NIFTI file has a different dimension from DWI.

looking for a matched dimension from loaded t1wt2w.

find a matched dimension from loaded t1wt2w.

seed=/Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/dsi/roi/seed.nii.gz

read region from /Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/dsi/roi/seed.nii.gz

T1T2 dimension: (260,311,260)

T1T2 voxel size: 0.7 0.7 0.7 

DWI dimension=(182,217,182)

NIFTI dimension=(260,311,260)

nifti loaded as single ROI file

NIFTI file has a different dimension from DWI.

looking for a matched dimension from loaded t1wt2w.

find a matched dimension from loaded t1wt2w.

start tracking.

finished tracking.

3000000 tracts are generated using 7736273 seeds.

0 tracts are removed by pruning.

The final analysis results in 3000000 tracts.

output=/Users/mudathirbakhit/Documents/13A-Laterality/Data/105115/dsi/tracts/all.tt.gz

saving all.tt.gz

Running whole brain tractography for 

DSI Studio Jun 21 2021, Fang-Cheng Yeh

source=/Users/mudathirbakhit/Documents/13A-Laterality/Data//T1w/DWI/*.fib.gz

action=trk

searching *.fib.gz in directory /Users/mudathirbakhit/Documents/13A-Laterality/Data//T1w/DWI

found 0 files.

On Thursday, July 8, 2021 at 11:10:36 PM UTC+9 Frank Yeh wrote:

[mudat...@gmail.com]

The problem was solved by updating to the last version of dsi studio

Thanks

Mudathir