Dear CONN experts,
I have preprocessed a dataset using the "preprocessing pipeline for surface-based (in subject-space) using nonlinear coregistration." The structural images were brain.mgz files generated by FreeSurfer and aseg.mgz files were also incorporated. After the preprocessing, I noticed in the "Setup > ROIs" section that the gray matter, white matter, and CSF (c{1,2,3}_aseg.img respectively) were all pointed to "unsmoothed functional data (secondary dataset #1)." In the "Setup > Other imaging data" section, those unsmoothed functional data pointed to ww*.surf.nii, which I assume were functional data resampled on the cortical surface. Now my questions are:
1) Can I go ahead with this automatic configuration? Does CONN try to extract CSF signals from the cortical surface (!?) or automatically identify the corresponding volume-based functional data and extract the signal therein?
2) Or should I manually point the GM/WM/CSF ROIs to "subject-space functional data" also generated by the pipeline (ww*.nii with no "surf" in the file name) available in the Other imaging data section?
Thanks in advance for your help!
Sincerely,
Michelle
Dear Michelle,
You are exactly right, you should point these volume-level ROIs to extract BOLD signal from your "subject-space functional data" dataset (or any other appropriate volume-level functional data file). In general when running surface-level analyses, and possibly mixing volume- and surface- level ROIs or data files, each individual ROI should point to the appropriate (same-space / same-level) BOLD signal source (this of course also applies to those cases when one is running volume-level analyses but is mixing ROIs across different spaces, e.g. some ROIs in MNI-space and others in subject- space). In your case that means pointing the Gray/White/CSF ROIs to the extract the BOLD signal from those same functional files but without the ".surf" in the filename.
Hope this helps
Alfonso
Originally posted by Michelle Cheng:
Dear CONN experts,
I have preprocessed a dataset using the "preprocessing pipeline for surface-based (in subject-space) using nonlinear coregistration." The structural images were brain.mgz files generated by FreeSurfer and aseg.mgz files were also incorporated. After the preprocessing, I noticed in the "Setup > ROIs" section that the gray matter, white matter, and CSF (c{1,2,3}_aseg.img respectively) were all pointed to "unsmoothed functional data (secondary dataset #1)." In the "Setup > Other imaging data" section, those unsmoothed functional data pointed to ww*.surf.nii, which I assume were functional data resampled on the cortical surface. Now my questions are:
1) Can I go ahead with this automatic configuration? Does CONN try to extract CSF signals from the cortical surface (!?) or automatically identify the corresponding volume-based functional data and extract the signal therein?
2) Or should I manually point the GM/WM/CSF ROIs to "subject-space functional data" also generated by the pipeline (ww*.nii with no "surf" in the file name) available in the Other imaging data section?
Thanks in advance for your help!
Sincerely,
Michelle
Dear Alfonso,
Thank you for clarifying my questions. This saved my day!
Sincerely,
Michelle
Originally posted by Alfonso Nieto-Castanon:
Dear Michelle,
You are exactly right, you should point these volume-level ROIs to extract BOLD signal from your "subject-space functional data" dataset (or any other appropriate volume-level functional data file). In general when running surface-level analyses, and possibly mixing volume- and surface- level ROIs or data files, each individual ROI should point to the appropriate (same-space / same-level) BOLD signal source (this of course also applies to those cases when one is running volume-level analyses but is mixing ROIs across different spaces, e.g. some ROIs in MNI-space and others in subject- space). In your case that means pointing the Gray/White/CSF ROIs to the extract the BOLD signal from those same functional files but without the ".surf" in the filename.
Hope this helps
Alfonso
Originally posted by Michelle Cheng:
Dear CONN experts,
I have preprocessed a dataset using the "preprocessing pipeline for surface-based (in subject-space) using nonlinear coregistration." The structural images were brain.mgz files generated by FreeSurfer and aseg.mgz files were also incorporated. After the preprocessing, I noticed in the "Setup > ROIs" section that the gray matter, white matter, and CSF (c{1,2,3}_aseg.img respectively) were all pointed to "unsmoothed functional data (secondary dataset #1)." In the "Setup > Other imaging data" section, those unsmoothed functional data pointed to ww*.surf.nii, which I assume were functional data resampled on the cortical surface. Now my questions are:
1) Can I go ahead with this automatic configuration? Does CONN try to extract CSF signals from the cortical surface (!?) or automatically identify the corresponding volume-based functional data and extract the signal therein?
2) Or should I manually point the GM/WM/CSF ROIs to "subject-space functional data" also generated by the pipeline (ww*.nii with no "surf" in the file name) available in the Other imaging data section?
Thanks in advance for your help!
Sincerely,
Michelle