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

Hi,
Could you tell me what's the input images? The original images or the preprocessed images? 
Thanks
Ivan

Hi Georgia,
I believe you are referring to the ArtRepair toolbox (https://www.nitrc.org/projects/art_repai...) instead of ART?
Best
Alfonso

Originally posted by Georgia O'Callaghan:

Hi Ivan,
Typically you would input the images after spatial realignment and coregistration/normalization (but before spatial smoothing)
Best
Alfonso

Originally posted by Yang Yang:

Hi Alfonso,
Thank you very much for your immediate reply. I have another questions: firstly, I found the default rotation threshold  is 0.02, but I am not sure what is the unit of this threshold, degree?. Secondly, the motion is closely related to task in my experiment. So, the  signal-task correlation is more than 0.2 (see attached example). But, I don't know whether it is a high rate. Could you share me some experience about that.
Thanks a lot in advance！
Ivan

Hi, 

Yes you are right - I was experimenting with different tool boxes so I had used both Art and ArtRepair and mixed up the outputs - I seem to have posted in the wrong forum! I apologize. 

Still if there is anybody who could give me advice I would really appreciate it. I have been reading around and came across some recommendations for artifact repairing that I wanted to try - they said to take the preprocessed images and deweight the scans with excess movement & enter the output of this into the design matrix. I tried importing the art_deweighted.txt into 'regressors' in an SPM8 batch (I also put my motion parameter's file into 'multiple regressors', as the recommendations suggested) but it wouldn't run because the txt file was a 1 x 22 vector when I had 445 scans.

I created a new txt file with 0's for all of the normal scans & 1 for the deweighted scans (making it 1 x 445) and put that in & it ran - but I'm not sure if that's the right thing to do? The original art_deweighted.txt file had the exact scan names in it, not 0's & 1's. 

I'm doing fMRI analysis for the first time & unfortunately my supervisor has never used it before either so I don't have someone in college to ask for help :S

Hi Alfonso,
I found there were no any outliers for my data. So, do I need to enter the file of 'art_regression_outliers_and_movement_*.mat' as covariate in the first-level analyses?  Moreover, I checked the rp_*.txt file resulted from relignment in SPM and I found the max motion of  several subjects was above 3 mm and 3 degree.  Does it mean that the threshold of  ART is more tolerant?
Best,
Ivan

Originally posted by Georgia O'Callaghan: 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,

Thank you,
yue Qi