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help > Questions about Harvard-Oxford Subcortical parcellation used for Conn toolbox
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Jan 18, 2018 07:01 PM | Joey Contreras - IU School of Medicine
Questions about Harvard-Oxford Subcortical parcellation used for Conn toolbox
Hello
I have some questions regarding the default atlas used in CONN. I am trying to identify certain subcortical structures using the HarvardOxfrod_Subcortical.xml file (attached in this email for reference) and am finding that the atlas.nii file contained within the ROI files of the CONN toolbox does not match up with the label index of the file. Could you please provide the correct Harvard-Oxford lookup table for subcortical structures?
I have some questions regarding the default atlas used in CONN. I am trying to identify certain subcortical structures using the HarvardOxfrod_Subcortical.xml file (attached in this email for reference) and am finding that the atlas.nii file contained within the ROI files of the CONN toolbox does not match up with the label index of the file. Could you please provide the correct Harvard-Oxford lookup table for subcortical structures?
Nov 4, 2018 04:11 AM | SHUN YAO - Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School
RE: Questions about Harvard-Oxford Subcortical parcellation used for Conn toolbox
I am also curious about the atlas built-in CONN toolbox.
Could somebody give me a label or index of the atlas in COON?
Because I'd like to select specific brain regions to be as a new ROI
Thank you very much
Could somebody give me a label or index of the atlas in COON?
Because I'd like to select specific brain regions to be as a new ROI
Thank you very much
Nov 4, 2018 04:11 PM | Daniel Berge - Hospital del Mar Medical Research Institute (IMIM)
RE: Questions about Harvard-Oxford Subcortical parcellation used for Conn toolbox
I am not sure if this will answer your question or you already knew
that. If you go to your conn folder, then /rois/, there you will
find the files atlas.txt and atlas.info that may clarify some of
these issues.
Hope this helps.
Hope this helps.
Nov 5, 2018 06:11 PM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: Questions about Harvard-Oxford Subcortical parcellation used for Conn toolbox
Just adding to Daniel's reply:
The atlas.info file will give you the details of how the atlas file in Conn was created by merging ROIs across Harvard-Oxford cortical and subcortical atlases and the cerebellar parcellations from the AAL atlas. The text file also mentions how discrepancies are resolved and the relevant references.
The atlas.txt file is a lookup file. Each line in this text file refers to a region in the atlas.nii file. For example, line 1 FP r (Frontal Pole right) corresponds to region number 1 in the NIfTI file (i.e. the atlas.nii file with intensity=1 is the right frontal pole).
Best
Pravesh
Originally posted by Daniel Berge:
The atlas.info file will give you the details of how the atlas file in Conn was created by merging ROIs across Harvard-Oxford cortical and subcortical atlases and the cerebellar parcellations from the AAL atlas. The text file also mentions how discrepancies are resolved and the relevant references.
The atlas.txt file is a lookup file. Each line in this text file refers to a region in the atlas.nii file. For example, line 1 FP r (Frontal Pole right) corresponds to region number 1 in the NIfTI file (i.e. the atlas.nii file with intensity=1 is the right frontal pole).
Best
Pravesh
Originally posted by Daniel Berge:
I am not sure if this will answer your question
or you already knew that. If you go to your conn folder, then
/rois/, there you will find the files atlas.txt and atlas.info that
may clarify some of these issues.
Hope this helps.
Hope this helps.