NITRC Artifact Detection Tools (ART) Forum: help

RE: ArtRepair Error / Art Detection vs ArtRepair

Anna Banaszkiewicz — Tue, 17 Sep 2024 12:49:54 GMT

Hi Kelly, 
I'm getting the same error for art_addmargin for few participants and runs. While in case of one of the participants I think it makes sense, in case of others I'm not sure what's happening. Did you manage to solve the problem and would be willing to share it here? 
Best wishes  -Anna

Execute art.m to generate Regressor files WITHOUT GUI

Stefan Radonjic — Wed, 24 Jan 2024 11:29:47 GMT

Hi everyone,
I am writing a fMRI processing pipeline in Python and I am using wrapper functions to call various MATLAB scripts (including SPM). Problem I am currently having is that I want to execute ART for outlier detection, but I CANNOT use GUI within my system.
How can I turn off the GUI option and just perform the MAIN PROCESS (i.e., outlier detection) where I can get: Regressor Files and Analysis Mask which ART should output for each subject?
I've attached the art.m script I am currently using (which relies on GUI)
I appreciate ANY help! Thanks!

RE: Art Summary Error - Index exceeds matrix

Idil Gemici — Tue, 31 Jan 2023 11:30:29 GMT

Hello,

Did you find any solution to this? I am currently dealing with the same problem.

Many thanks!

RE: What do I do with the output?

Yue Qi — Mon, 07 Nov 2022 3:35:26 GMT

[i]Originally posted by Georgia O'Callaghan:[/i][quote]Hi there!

I have followed the ArtRepair instructions and get the following output files (in addition to my 'v' prefix files): ArtifactMask.nii, art_deweighted.txt & art_repaired.txt, the instructions I read said that these files can then be entered in the design specification stage as regressors but it doesn't go into any more detail than that - I don't know what to do! Please help!

I have opened the SPM batch editor & selected 'fMRI model specification', would the two text files go into 'Regressors' under 'Data & Design' along with your 'rp.txt' motion parameters file? Is it as simple as that? What should I do with the 'ArtifactMask.nii'?

Any advice would be greatly appreciated,

Thank you,

Georgia[/quote][color=#000000]hi georiga, I have the same question with you，have you solved it？did you finished the art——summary？Any advice would be greatly appreciated,[/color]

Thank you,
yue Qi

RE: Calculation and... What next?

Shubin Li — Sun, 27 Feb 2022 15:53:11 GMT

I have the same question! May I know if you already figure out what to do next? Please help me. My email: amberli 9634@outlook.com. Really really thank you.

RE: thresholds for mouse data

Vikram Rao — Fri, 09 Oct 2020 3:06:57 GMT

Just wanted to check again to see what thresholds to use for mice data. Our mice data are 0.05mm iso

ART maximum limit

Janelle Foret — Tue, 25 Aug 2020 19:17:24 GMT

Is there a maximum limit for scrubbed time points "removal" set by the ART outlier detection tool? My understanding is that time points aren't really removed but are still disregarded in analyses but was not finding out if there is a certain percentage of time points identified that leads to automatic exclusion of a subject from the analyses.

If this maximum limit exists and can be adjusted by the researcher, I must have missed it and am just wanting to know what the default maximum would be.

Thank you!

RE: art batch

Bianca Leonard — Mon, 27 Jul 2020 22:15:22 GMT

[color=#000000]Hello all, [/color]

[color=#000000]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.[/color]

[color=#000000]Your help is appreciated. [/color]

[color=#000000]Thanks![/color]

[color=#000000]Bianca[/color]

[i]Originally posted by Emiliana Tonini:[/i][quote]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)[/quote]

RE: ArtRepair Error / Art Detection vs ArtRepair

Kelly Hiersche — Mon, 13 Jul 2020 16:04:01 GMT

Hello,

I am just checking in to see if anyone has any ideas why I may be seeing this problem.

Thanks,

Kelly

Clarification on what are Max Motion Values from Art Toolbox

Victoria Okuneye — Mon, 08 Jun 2020 16:24:40 GMT

Hello,

I would appreciate getting insight on the QA_MaxMotion co-variate in CONN.

I used a Max Motion threshold value of 3 to exclude participants in my study.

I inferred that this was a 3mm max motion cut off. Was I wrong in this?

A review asked about rotation threshold and I realize am not sure how max motion is evaluating both rotation and translation, nor certainity on it's units for the conn project.

Best,
Victoria