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help > RE: using ART with slice timing corrected files
Sep 14, 2015 09:09 PM | Alfonso Nieto-Castanon - Boston University
RE: using ART with slice timing corrected files
Hi Catherine,
Yes, that is perfectly fine. Just make sure to either: a) enter your rp_*.txt files as a first-level covariate named 'realignment' into CONN; or b) make sure those rp_*.txt files are in the same directory as your functional volumes.This needs to be done before running ART just so that ART knows where to find the subject movement files it needs to find potential outlier scans.
And regarding how to remove the first four functional volumes, either of the following approaches would work:
a) if entering your functional volumes using the GUI select the 'spm_select' option in the top-right corner so that you can directly identify the individual 3d volumes within your 4d data file that you want to enter into CONN (e.g. select 5:N volumes instead of 1:N to disregard the first four volumes)
b) if entering your functional volumes using batch scripts simply enter the individual 3d volumes to be included in CONN as a cell array (e.g. enter something like {'data.nii,5','data.nii,6','data.nii,7'....} to disreagrd the first four volumes)
c) if you have already entered your functional volumes into CONN, go to either 'Preprocessing' or to 'Setup.Functionals.FunctionalTools', select there the option that reads something like 'remove initial scans', and enter the number of scans that you want to remove (e.g. 4; and remember to save your project afterwards to save these changes)
Hope this helps
Alfonso
Originally posted by Catherine Hubbard:
Yes, that is perfectly fine. Just make sure to either: a) enter your rp_*.txt files as a first-level covariate named 'realignment' into CONN; or b) make sure those rp_*.txt files are in the same directory as your functional volumes.This needs to be done before running ART just so that ART knows where to find the subject movement files it needs to find potential outlier scans.
And regarding how to remove the first four functional volumes, either of the following approaches would work:
a) if entering your functional volumes using the GUI select the 'spm_select' option in the top-right corner so that you can directly identify the individual 3d volumes within your 4d data file that you want to enter into CONN (e.g. select 5:N volumes instead of 1:N to disregard the first four volumes)
b) if entering your functional volumes using batch scripts simply enter the individual 3d volumes to be included in CONN as a cell array (e.g. enter something like {'data.nii,5','data.nii,6','data.nii,7'....} to disreagrd the first four volumes)
c) if you have already entered your functional volumes into CONN, go to either 'Preprocessing' or to 'Setup.Functionals.FunctionalTools', select there the option that reads something like 'remove initial scans', and enter the number of scans that you want to remove (e.g. 4; and remember to save your project afterwards to save these changes)
Hope this helps
Alfonso
Originally posted by Catherine Hubbard:
Hi,
I would like to use ART and then add the output files to the confound list for the denoising step in CONN to my already preprocessed rs-fmri files that have been slice time corrected, realigned, segmented, normalized and smoothed in SPM, is this a problem? or is this just an issue if I use the depsiking option? I plan to specify the swra*.nii files for my preprocessed functional images and the wT1.nii for my structural images. I would add the rp*a.nii and the outliers.mat file to the confound list in the denoising tab to regress these out. After that I plan to perform 1st level analysis in CONN and then 2nd level analysis in SPM.
Another question I have is whether it is possible to remove the first four volumes in CONN prior to performing the denoising step on my data that has already been preprocessed in SPM?
Thanks!
I would like to use ART and then add the output files to the confound list for the denoising step in CONN to my already preprocessed rs-fmri files that have been slice time corrected, realigned, segmented, normalized and smoothed in SPM, is this a problem? or is this just an issue if I use the depsiking option? I plan to specify the swra*.nii files for my preprocessed functional images and the wT1.nii for my structural images. I would add the rp*a.nii and the outliers.mat file to the confound list in the denoising tab to regress these out. After that I plan to perform 1st level analysis in CONN and then 2nd level analysis in SPM.
Another question I have is whether it is possible to remove the first four volumes in CONN prior to performing the denoising step on my data that has already been preprocessed in SPM?
Thanks!
Threaded View
| Title | Author | Date |
|---|---|---|
| Catherine Hubbard | Sep 10, 2015 | |
| Alfonso Nieto-Castanon | Sep 14, 2015 | |
| Melanie Morrison | Feb 5, 2020 | |
| Alfonso Nieto-Castanon | Feb 5, 2020 | |
| Catherine Hubbard | Sep 16, 2015 | |
| Alfonso Nieto-Castanon | Sep 18, 2015 | |
| Catherine Hubbard | Sep 18, 2015 | |
| Catherine Hubbard | Sep 18, 2015 | |
| Alfonso Nieto-Castanon | Sep 26, 2015 | |