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help > RE: atlas.nii in CONN does not match fmriprep preprocessed T1
Aug 26, 2020 06:08 PM | Dong An
RE: atlas.nii in CONN does not match fmriprep preprocessed T1
Originally posted by Pravesh Parekh:
Thank you very much for your reply. I was wondering if you mean even my fmriprep output is MNI152Lin2009cAsym space, the Harvard-Oxford atlas would automatically adjusted, and thus the different dimension would not affact final coordinates? Do I need to resample Hardvard-Oxford atlas to 193*229*193 first, then import resampled Hardvard-Oxford atlas into CONN before fuctional connectivity analysis?
Thank you,
Xinyuan
Hello,
To the best of my knowledge, Conn handles affine transforms between coordinates so that they line up across images even if their dimensions differ (see conn_convertcoordinates.m). However, you might want to make sure that the output space from fmriprep is compatible with the atlas that you want to use (i.e. the standard spaces are comparable); you wouldn't want a situation where the standard spaces are not directly comparable: imagine a situation where one standard space has slightly more deformation in a part of the brain which does not linearly map to another standard space. There is some discussion on Harvard-Oxford parcellation and their comparison to different standard spaces here and here.
Hope this helps
Best
Pravesh
Originally posted by Dong An:
Dear Pravesh,To the best of my knowledge, Conn handles affine transforms between coordinates so that they line up across images even if their dimensions differ (see conn_convertcoordinates.m). However, you might want to make sure that the output space from fmriprep is compatible with the atlas that you want to use (i.e. the standard spaces are comparable); you wouldn't want a situation where the standard spaces are not directly comparable: imagine a situation where one standard space has slightly more deformation in a part of the brain which does not linearly map to another standard space. There is some discussion on Harvard-Oxford parcellation and their comparison to different standard spaces here and here.
Hope this helps
Best
Pravesh
Originally posted by Dong An:
Dear Alfonso,
I did preprocessing in fmriprep, and then imported fmriprep output into CONN. I found the dimension of atlas.nii is different from that of fmriprep output. The Harvard-Oxford atlas.nii used by default in CONN is 182*218*182,while the dimension of fmriprep preprocessed T1 (sub-01_space-MNI152Lin2009cAsym_desc-preproc_T1.nii) is 193*229*193. May I ask if this dimension difference would affect funtional connectivity results (eg, the coordinate of peak voxel)?
Thank you very much for your help in advance!
Xinyuan
I did preprocessing in fmriprep, and then imported fmriprep output into CONN. I found the dimension of atlas.nii is different from that of fmriprep output. The Harvard-Oxford atlas.nii used by default in CONN is 182*218*182,while the dimension of fmriprep preprocessed T1 (sub-01_space-MNI152Lin2009cAsym_desc-preproc_T1.nii) is 193*229*193. May I ask if this dimension difference would affect funtional connectivity results (eg, the coordinate of peak voxel)?
Thank you very much for your help in advance!
Xinyuan
Thank you very much for your reply. I was wondering if you mean even my fmriprep output is MNI152Lin2009cAsym space, the Harvard-Oxford atlas would automatically adjusted, and thus the different dimension would not affact final coordinates? Do I need to resample Hardvard-Oxford atlas to 193*229*193 first, then import resampled Hardvard-Oxford atlas into CONN before fuctional connectivity analysis?
Thank you,
Xinyuan
Threaded View
| Title | Author | Date |
|---|---|---|
| Dong An | Aug 25, 2020 | |
| Pravesh Parekh | Aug 25, 2020 | |
| Dong An | Aug 26, 2020 | |