SCT 5.1 - SCT_Run_Batch

SCT
1

Hi,
Would you please look at this code. Nothing happen in result .

Thanks

ranginkamon@ubuntu:~$ '/home/ranginkamon/sct_5.1.0/bin/sct_run_batch'  -jobs -1 -path-data  '/home/ranginkamon/sub-tehran07/'   -path-output ~/spineGeneric_results/ -script '/home/ranginkamon/spine-generic/process_data.sh' 

--
Spinal Cord Toolbox (5.1.0)

sct_run_batch -jobs -1 -path-data /home/ranginkamon/sub-tehran07/ -path-output /home/ranginkamon/spineGeneric_results/ -script /home/ranginkamon/spine-generic/process_data.sh
--

INFO SYSTEM
-----------
OS: linux (Linux-5.4.0-42-generic-x86_64-with-debian-bullseye-sid)
CPU cores: Available: 8 | Threads used by ITK Programs: 1
RAM: Total 3166 MB | Available 1330 MB | Used 1549 MB

INPUT ARGUMENTS
---------------
batch_log: sct_run_batch_log.txt
config: null
continue_on_error: 1
email_from: null
email_host: smtp.gmail.com:587
email_to: null
exclude: null
exclude_list: null
include: null
include_list: null
itk_threads: 1
jobs: -1
path_data: /home/ranginkamon/sub-tehran07/
path_output: /home/ranginkamon/spineGeneric_results/
path_segmanual: .
script: /home/ranginkamon/spine-generic/process_data.sh
script_args: ''
subject_prefix: sub-
v: 1
zip: false

SCRIPT
------
git commit: 75c7f0c93c3012fd88be3af7d836b0c868af7bd1
git origin: https://github.com/spine-generic/spine-generic.git
Copying script to output folder...
/home/ranginkamon/spine-generic/process_data.sh -> /home/ranginkamon/spineGeneric_results/process_data.sh
Setting execute permissions for script file /home/ranginkamon/spine-generic/process_data.sh ...

DATA
----
git commit: ?!?
git origin: ?!?

RUNNING
-------
Processing 0 subjects in parallel. (Worker processes used: 7).

Hooray! your batch completed successfully :-)

Started: 06h47m19s | Ended: 06h47m19s | Duration: 00h00m00s

To open the Quality Control (QC) report on a web-browser, run the following:
xdg-open /home/ranginkamon/spineGeneric_results/qc/index.html
2

It didn’t find any subject to process inside your path:

Processing 0 subjects

Subject folders should start with sub- as instructed by the parameter subject_prefix.

What is the output of:

ls /home/ranginkamon/sub-tehran07/
3

Untitled
Untitled731×500 50.2 KB

4

“ls” would be easier because your file names are truncated. But anyway, the path_data should point to the folder that contains the subject, not point to the subject folder directly.

E.g. in the case of the spine-generic project, path_data would be data-multi-subject, not sub-ubc06.

5

OK, I will do it again. Thanks.

6

It works well. Thanks.

7

Dear Prof. Kohen

I got the below table last year from SCT v4.2 , but now I could not remember the code to get this result. Could you please help me how to extract this table from my data.

Thanks.

mtr_in_wm.xlsx (55.8 KB)

8

I got the below table last year from SCT v4.2 , but now I could not remember the code to get this result. Could you please help me how to extract this table from my data.

you can use sct_extract_metric. More information in the example batch_processing script.

Also, this issue is different from the main thread (which is about using sct_run_batch)-- if you have question on another topic, please open another specific issue. Thank you.

9

Yes you are right sorry for that.

Thanks for response.