Exporting tract stats on multiple TRK files

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Artur Vetkas

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Jan 5, 2023, 10:21:16 PM1/5/23
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Hi!

Is there a way to efficiently export stats on multiple .trk.gz files through console? I tried the same approach as when merge but it did not work.

--action=ana --source=HCP1065.1mm.fib.gz --tract=AC.trk.gz,AF_L.trk.gz --export=stat


Thanks in advance

Fang-Cheng Yeh

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Jan 5, 2023, 10:39:38 PM1/5/23
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Could you post the console output?
There might be a hint why it didn't work

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Artur Vetkas

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Jan 6, 2023, 9:08:21 AM1/6/23
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The code i used is: --action=ana --source=HCP1065.1mm.fib.gz --tract=AC.trk.gz,AF_L.trk.gz,AF_R.trk.gz,AR_L.trk.gz,AR_R.trk.gz --export=stat

The console loads of the tracts and show the count, but runs the statistics and the outputs only the first.

'

source=HCP1065.1mm.fib.gz

action=ana

loop=HCP1065.1mm.fib.gz

+ run ana

| loading HCP1065.1mm.fib.gz...

| + open FIB file

| | + opening HCP1065.1mm.fib.gz

| | |_1.69 s

| | + loading fiber and image data

| | | + loading image volumes

| | | |_209 ms

| | | + initiating data

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

| | | | |_2 ms

| | | | matched template (by image size): ICBM152_adult

| | | |_25 ms

| | |_259 ms

| | FIB file loaded

| |_1.979 s

| tract=AC.trk.gz,AF_L.trk.gz,AF_R.trk.gz,AR_L.trk.gz,AR_R.trk.gz

| + loading AC.trk.gz

| |_1.475 s

| A total of 10302 tracks loaded

| + loading AF_L.trk.gz

| |_2.295 s

| A total of 34156 tracks loaded

| + loading AF_R.trk.gz

| |_204 ms

| A total of 3356 tracks loaded

| + loading AR_L.trk.gz

| |_62 ms

| A total of 2252 tracks loaded

| + loading AR_R.trk.gz

| |_16 ms

| A total of 654 tracks loaded

| a total of 5 tract file(s) loaded

| + post-tracking analysis

| | export=stat

| | export statistics to AC.trk.gz.stat.txt

| | region dimension: (125,151,108)

| | region voxel size: 1.25 1.25 1.25

| | region voxel count: 4942

| | region dimension: (125,151,108)

| | region voxel size: 1.25 1.25 1.25

| | region voxel count: 3644

| | nrdi04L loaded

| | [thread]dti_fa loaded

| | [thread]ad loaded

| | [thread]rdi loaded

| | [thread]nrdi04L loaded

| | [thread]gfa loaded

| | [thread]rdi loaded

| | [thread]md loaded

| | [thread]rd loaded

| | [thread]nrdi02L loaded

| | [thread]nrdi02L loaded

| | [thread]nrdi06L loaded

| | nrdi06L loaded

| | [thread]iso loaded

| |_11.995 s

|_18.542 s

Fang-Cheng Yeh

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Jan 7, 2023, 10:54:12 PM1/7/23
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Thank you for sending the details.
The quick solution is to call the command multiple time, with each for each track.

Best
Frank

Artur Vetkas

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Jan 15, 2023, 10:23:14 AM1/15/23
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Thanks for the response! 
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