help
help > RE: Native-space analysis with FreeSurfer segment
Nov 25, 2015 04:11 PM | Alfonso Nieto-Castanon - Boston University
RE: Native-space analysis with FreeSurfer segment
Hi Athena,
If you have processed your subjects anatomical data in FreeSurfer you can very easily import that into CONN to import that info and run all of your analyses on those cortical surfaces. To do this:
1) in the Setup.Structurals tab select for each subject the anatomical files in the freesurfer-generated subject*/mri/ folder (e.g. the T1.mgz or .mgh files there) and CONN will automatically import each subject's surface information and it will offer you the choice to also import the corresponding gray/white/CSF masks from the aseg.mgz files (or if you are using batch scripts you may also use the conn_importaseg script to automaticlaly import those masks)
2) set the 'Analysis space' option in the Setup.Options tab to 'surface (FreeSurfer fsaverage)'
3) If you also have a *.annot file with your choice of ROIs defined on the fsaverage space you may also add those to the list of ROIs in Setup.ROIs. You may also enter there other subject-specific *.img/.nii/.mgh ROIs that you may have (note that if you have all of your data in subject-space you should not be using any MNI-space ROIs and your ROIs should be in subject-space as well)
4) last, make sure you run one of the "subject-space" preprocessing pipelines (instead of the "MNI-space" preprocessing pipelines) so your functional data is kept in subject-space and appropriately coregistered to the FreeSurfer-generated surfaces
Hope this helps
Alfonso
Originally posted by Athena Demertzi:
If you have processed your subjects anatomical data in FreeSurfer you can very easily import that into CONN to import that info and run all of your analyses on those cortical surfaces. To do this:
1) in the Setup.Structurals tab select for each subject the anatomical files in the freesurfer-generated subject*/mri/ folder (e.g. the T1.mgz or .mgh files there) and CONN will automatically import each subject's surface information and it will offer you the choice to also import the corresponding gray/white/CSF masks from the aseg.mgz files (or if you are using batch scripts you may also use the conn_importaseg script to automaticlaly import those masks)
2) set the 'Analysis space' option in the Setup.Options tab to 'surface (FreeSurfer fsaverage)'
3) If you also have a *.annot file with your choice of ROIs defined on the fsaverage space you may also add those to the list of ROIs in Setup.ROIs. You may also enter there other subject-specific *.img/.nii/.mgh ROIs that you may have (note that if you have all of your data in subject-space you should not be using any MNI-space ROIs and your ROIs should be in subject-space as well)
4) last, make sure you run one of the "subject-space" preprocessing pipelines (instead of the "MNI-space" preprocessing pipelines) so your functional data is kept in subject-space and appropriately coregistered to the FreeSurfer-generated surfaces
Hope this helps
Alfonso
Originally posted by Athena Demertzi:
Hello,
I would like to perform resting state connectivity (seed-to-voxel) analysis at each subject's native space. Since my population is characterized by brain pathologies, I was thinking to use FreeSurfer's reconstruction algorithms for optimal segmentation (it also allows for manual corrections of defects).
If I am to do that, could I still use Conn for data denoising? I mean to say, which FreeSurfer images are the equivalent for the gray matter, white matter and CSF? Maybe other tips that could be helpful as well?
Thank you so much in advance!
Best,
Athena
I would like to perform resting state connectivity (seed-to-voxel) analysis at each subject's native space. Since my population is characterized by brain pathologies, I was thinking to use FreeSurfer's reconstruction algorithms for optimal segmentation (it also allows for manual corrections of defects).
If I am to do that, could I still use Conn for data denoising? I mean to say, which FreeSurfer images are the equivalent for the gray matter, white matter and CSF? Maybe other tips that could be helpful as well?
Thank you so much in advance!
Best,
Athena
Threaded View
Title | Author | Date |
---|---|---|
Athena Demertzi | Nov 24, 2015 | |
Alfonso Nieto-Castanon | Nov 25, 2015 | |
Alex G | May 26, 2022 | |
derya | Oct 12, 2022 | |
Athena Demertzi | Nov 26, 2015 | |
Alfonso Nieto-Castanon | Nov 26, 2015 | |