help > RE: art batch
Jul 27, 2020  03:07 PM | Bianca Leonard
RE: art batch
Hello all, 

Following up if anyone has found a way to batch this process? I am trying to feed it multiple subjects, but cannot seem to find the proper structure that the batch will accept. I think it might be an issue in the way I have the names listed out, but I can't seem to find the proper way to do it online.

Your help is appreciated. 


Thanks!

Bianca

Originally posted by Emiliana Tonini:
Dear all, 

Is it possible to create a batch with ART in order to automatically run the outliers detection analysis on multiple subjects without using the GUI ?

Looking at the ART documentation, it seems to be possible to use something with the following arguments, but I'm having trouble finding the needed structure of the script itself. Is there an example available ?

Thank you very much! 

Best regards, 
Emiliana


% art('sess_file','filename.cfg');
% Uses the configuration file filename.cfg to define the art analysis
% Options: see example.cfg file for more information
%
% art('sess_file',batch)
% Uses the structure batch to define the art analysis
% Options:
% batch.P : batch.P{nses} [char] functional filename(s) for session nses
% batch.M : batch.M{nses} [char] realignment filename for session nses
% batch.global_threshold : global BOLD signal threshold (z-score)
% batch.motion_threshold : motion threshold(s)
% batch.use_diff_motion : 1/0 use scan-to-scan differences in motion parameters
% batch.use_diff_global : 1/0 use scan-to-scan differences in global BOLD signal
% batch.use_norms : 1/0 use motion composite measure
% batch.drop_flag : number of initial scans to flag as outliers (removal of initial scans)
% batch.motion_file_type : indicates type of realignment file (0: SPM rp_*.txt file; 1: FSL .par file; 2: Siemens .txt file; 3: .txt SPM-format but rotation parameters in degrees)
% batch.output_dir : directory for output files (default same folder as first-session functional files)

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TitleAuthorDate
Emiliana Tonini Mar 24, 2019
RE: art batch
Bianca Leonard Jul 27, 2020