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help > RE: Using Freesurfer ROIs in Surface-based analysis
Apr 10, 2019 12:04 PM | Alfonso Nieto-Castanon - Boston University
RE: Using Freesurfer ROIs in Surface-based analysis
Hi Kaitlin
Simply enter that T1.mgz file as your structural data and coregister your functional to your structural data, for example using CONN's preprocessing step 'functional Direct coregistration to structural'.
Also, just for general reference, there are a few preprocessing pipelines in CONN specifically designed for surface-based analyses (those labeled 'preprocessing pipeline for surface-based analyses...' in the preprocessing gui), and those pipelines already include the above coregistration step, so in general you just need to enter your raw functional data (e.g. Func.nii) as well as your freesurfer-processed structural data (e.g. T1.mgz) into CONN, and then use directly one of those default preprocessing pipelines to make sure that everything is properly aligned for surface-based analyses.
Hope this helps
Alfonso
Originally posted by Kaitlin Cassady:
Simply enter that T1.mgz file as your structural data and coregister your functional to your structural data, for example using CONN's preprocessing step 'functional Direct coregistration to structural'.
Also, just for general reference, there are a few preprocessing pipelines in CONN specifically designed for surface-based analyses (those labeled 'preprocessing pipeline for surface-based analyses...' in the preprocessing gui), and those pipelines already include the above coregistration step, so in general you just need to enter your raw functional data (e.g. Func.nii) as well as your freesurfer-processed structural data (e.g. T1.mgz) into CONN, and then use directly one of those default preprocessing pipelines to make sure that everything is properly aligned for surface-based analyses.
Hope this helps
Alfonso
Originally posted by Kaitlin Cassady:
Hello!
I noticed in the CONN manual that if you are interested in performing surface-based ROI-to-ROI analyses, that you are supposed to use the subject-space non-smoothed functional image (i.e., auFunc.nii) and the subject space freesurfer structural ROIs (i.e., T1.mgz and aparc+aseg.mgz). My issue is that the non-smoothed functional (i.e., auFunc.nii") appears to NOT be in the same space as the subject's T1.mgz and aparc+aseg.gmz images. It DOES seem to be in the same space as my raw T1.nii file though. How can I get these three files in the same space?
Thanks!
Kaitlin
I noticed in the CONN manual that if you are interested in performing surface-based ROI-to-ROI analyses, that you are supposed to use the subject-space non-smoothed functional image (i.e., auFunc.nii) and the subject space freesurfer structural ROIs (i.e., T1.mgz and aparc+aseg.mgz). My issue is that the non-smoothed functional (i.e., auFunc.nii") appears to NOT be in the same space as the subject's T1.mgz and aparc+aseg.gmz images. It DOES seem to be in the same space as my raw T1.nii file though. How can I get these three files in the same space?
Thanks!
Kaitlin
Threaded View
| Title | Author | Date |
|---|---|---|
| Kaitlin Cassady | Apr 8, 2019 | |
| Alfonso Nieto-Castanon | Apr 10, 2019 | |
| Kaitlin Cassady | Apr 20, 2019 | |