help > What do I do with the output?
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Aug 28, 2014  09:08 AM | Georgia O'Callaghan - Trinity College Dublin
What do I do with the output?
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
Aug 31, 2014  10:08 PM | Yang Yang
RE: What do I do with the output?
Hi,
Could you tell me what's the input images? The original images or the preprocessed images? 
Thanks
Ivan
Aug 31, 2014  10:08 PM | Alfonso Nieto-Castanon - Boston University
RE: What do I do with the output?
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 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
Aug 31, 2014  10:08 PM | Alfonso Nieto-Castanon - Boston University
RE: What do I do with the output?
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,
Could you tell me what's the input images? The original images or the preprocessed images? 
Thanks
Ivan
Sep 1, 2014  12:09 AM | Yang Yang
RE: What do I do with the output?
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 advanceļ¼
Ivan
Sep 3, 2014  03:09 AM | Georgia O'Callaghan - Trinity College Dublin
RE: What do I do with the output?
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
Sep 5, 2014  07:09 PM | Yang Yang
RE: What do I do with the output?
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