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help > RE: Denoised Data Output Option Problem
May 13, 2016 04:05 AM | Alfonso Nieto-Castanon - Boston University
RE: Denoised Data Output Option Problem
Hi Jeff,
You could split those files using something like:
a = spm_vol('myfile.nii');
spm_file_merge(a(1:124), 'myfile_session1.nii');
spm_file_merge(a(125:248), 'myfile_session2.nii');
spm_file_merge(a(249:372), 'myfile_session3.nii');
And yes, those nifti files will be corrected by any effects that you have entered in the Denoising step (typically aCompCor white matter/CSF components, estimated subject motion parameters, outliers, constant and linear trends, as well as filtering). Scrubbing is effected by including the ART-defined outlier covariates in this removal step, so effectively those timepoints will be set to 0 (prior to filtering if using RegBP)
Hope this helps
Alfonso
Originally posted by Jeff Browndyke:
You could split those files using something like:
a = spm_vol('myfile.nii');
spm_file_merge(a(1:124), 'myfile_session1.nii');
spm_file_merge(a(125:248), 'myfile_session2.nii');
spm_file_merge(a(249:372), 'myfile_session3.nii');
And yes, those nifti files will be corrected by any effects that you have entered in the Denoising step (typically aCompCor white matter/CSF components, estimated subject motion parameters, outliers, constant and linear trends, as well as filtering). Scrubbing is effected by including the ART-defined outlier covariates in this removal step, so effectively those timepoints will be set to 0 (prior to filtering if using RegBP)
Hope this helps
Alfonso
Originally posted by Jeff Browndyke:
CONN produces denoised data files in NIFTI
format that are concatenated across sessions. I have three
sessions for most of my subjects and would like to separate out
these sessions that I can then enter into GIFT or REST software.
How does one separate out the concatenated denoised CONN
output files (e.g., 372 images = three 124 image sessions)?
Also, I would add...how does CONN handle the denoised output? Are these resulting NIFTI files corrected for both motion and signal artifacts? Are the signal artifact points scrubbed or substituted in the resulting data?
Jeff
Also, I would add...how does CONN handle the denoised output? Are these resulting NIFTI files corrected for both motion and signal artifacts? Are the signal artifact points scrubbed or substituted in the resulting data?
Jeff
Threaded View
| Title | Author | Date |
|---|---|---|
| Jeff Browndyke | May 11, 2016 | |
| Sebastian Speer | Oct 28, 2019 | |
| Alfonso Nieto-Castanon | May 13, 2016 | |
| Jeff Browndyke | Jun 9, 2016 | |
| Alfonso Nieto-Castanon | Jun 9, 2016 | |
| Jeff Browndyke | May 17, 2016 | |
| Lucas Moro | May 19, 2016 | |
| Jeff Browndyke | Jun 9, 2016 | |