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help > RE: loading ROIs of interest
Jan 11, 2012 06:01 AM | Alfonso Nieto-Castanon - Boston University
RE: loading ROIs of interest
Hi Moriah,
You can remove some ROIs from consideration by going to the Setup->Rois tab, right-clicking on the desired ROI from the 'ROIs' list and selecting 'remove selected ROIs'. In order to add new ROIs, in the same Setup->Rois tab, select the first empty space in the 'ROIs' list, then enter a new name in the 'ROI name' field, and then (for subject-independent ROIs) select all of the subjects in the 'Subjects' list and then select an ROI file in the 'Select ROI definition files' section. For subject-specific ROIs you could: a) select sequentially one subject from the 'Subjects' list and one ROI file from the 'Select ROI definition files' section -and repeat these for all subjects-; or b) select all subjects from the 'Subjects' list and then select the same number of ROI files (one ROI file per subject) from the 'Select ROI definition files' section. The errors that you describe are possibly due to some subjects missing the associated ROI file (to double-check this, simply select each ROI in the 'ROIs' list, and then click sequentially on each subject in the 'Subjects' list to make sure all of them have an associated ROI file). Let me know if this helps.
And regarding your second question, subject movement can have a dramatic confouding effect on connectivity measures (typically it introduces positive biases in the computation of connectivity values). I would recommend if possible to re-run the 'realignment' step on your functional volumes and enter the resulting realigned volumes as well as movement parameters into the analyses for all subjects (but I might be misinterpreting your question, I am not sure why you would have subject motion parameters for some subjects but not others; perhaps you used prospective motion correction in the scanner?)
Best regards
Alfonso
Originally posted by Moriah Thomason:
You can remove some ROIs from consideration by going to the Setup->Rois tab, right-clicking on the desired ROI from the 'ROIs' list and selecting 'remove selected ROIs'. In order to add new ROIs, in the same Setup->Rois tab, select the first empty space in the 'ROIs' list, then enter a new name in the 'ROI name' field, and then (for subject-independent ROIs) select all of the subjects in the 'Subjects' list and then select an ROI file in the 'Select ROI definition files' section. For subject-specific ROIs you could: a) select sequentially one subject from the 'Subjects' list and one ROI file from the 'Select ROI definition files' section -and repeat these for all subjects-; or b) select all subjects from the 'Subjects' list and then select the same number of ROI files (one ROI file per subject) from the 'Select ROI definition files' section. The errors that you describe are possibly due to some subjects missing the associated ROI file (to double-check this, simply select each ROI in the 'ROIs' list, and then click sequentially on each subject in the 'Subjects' list to make sure all of them have an associated ROI file). Let me know if this helps.
And regarding your second question, subject movement can have a dramatic confouding effect on connectivity measures (typically it introduces positive biases in the computation of connectivity values). I would recommend if possible to re-run the 'realignment' step on your functional volumes and enter the resulting realigned volumes as well as movement parameters into the analyses for all subjects (but I might be misinterpreting your question, I am not sure why you would have subject motion parameters for some subjects but not others; perhaps you used prospective motion correction in the scanner?)
Best regards
Alfonso
Originally posted by Moriah Thomason:
I would like to include rois I have made in the
analysis. I would like to remove from consideration the
default ROIs. WHen I remove BA.img form the roi folder, the
conn program will not open. When I remove it in the setup
stage in ROI-data-set-up, I am given errors that my ROIs have not
been defined.
(ERROR: Subject 2 ROI 2 file has not been defined )
when I go to select new ROIs in the selection window I am given the message "mismatched number of files"
Please advise about the proper way to consider only a select numebr of ROIs in this analyses.
Second, I have an unrelated question which is related to the fact that I do not have movement parameter files for all of my subjects. I wonder if I should include them as covariates for the 50% or so of subjects I have these for, or not.
thank you,
Moriah
(ERROR: Subject 2 ROI 2 file has not been defined )
when I go to select new ROIs in the selection window I am given the message "mismatched number of files"
Please advise about the proper way to consider only a select numebr of ROIs in this analyses.
Second, I have an unrelated question which is related to the fact that I do not have movement parameter files for all of my subjects. I wonder if I should include them as covariates for the 50% or so of subjects I have these for, or not.
thank you,
Moriah
Threaded View
| Title | Author | Date |
|---|---|---|
| Moriah Thomason | Dec 23, 2011 | |
| Alfonso Nieto-Castanon | Jan 11, 2012 | |
| Moriah Thomason | Jan 11, 2012 | |