Dear experts,
I'd like to use Neuromorphometrics atlas, which is found in
CAT12.
I input neuromorphometrics.nii file as ROI and click the atlas
option. However, after denoising, I found that CONN toolbox
identifies the atlas file as one ROI. Does anyone know how to solve
the problem?
Best regards,
Chih-Hao Lien
Hi Chih-Hao Lien
Sorry this atlas file labels are saved in a format that CONN is not able to interpret correctly. I am attaching the atlas converted to a CONN-compatible format. Unzip this file and re-import it into your CONN project, and let me know if you still run into any issues.
Hope this helps
Alfonso
Originally posted by Chihhao Lien:
Dear experts,
I'd like to use Neuromorphometrics atlas, which is found in CAT12.
I input neuromorphometrics.nii file as ROI and click the atlas option. However, after denoising, I found that CONN toolbox identifies the atlas file as one ROI. Does anyone know how to solve the problem?
Best regards,
Chih-Hao Lien
Hi Alfonso,
Sorry for the late reply and thank you for your help, it's helpful!
The atlas file works well!
However, I recently noticed that I couldn't find the ROI of the Left Inferior Lateral Ventricle while using the file (see the attached figure, please).
Could you help me check this issue?
Best regards,
Chih-Hao Lien
Originally posted by Alfonso Nieto-Castanon:
Hi Chih-Hao Lien
Sorry this atlas file labels are saved in a format that CONN is not able to interpret correctly. I am attaching the atlas converted to a CONN-compatible format. Unzip this file and re-import it into your CONN project, and let me know if you still run into any issues.
Hope this helps
Alfonso
Originally posted by Chihhao Lien:
Dear experts,
I'd like to use Neuromorphometrics atlas, which is found in CAT12.
I input neuromorphometrics.nii file as ROI and click the atlas option. However, after denoising, I found that CONN toolbox identifies the atlas file as one ROI. Does anyone know how to solve the problem?
Best regards,
Chih-Hao Lien
Hi Alfonso,
I checked my problem again, and I'd like to provide more
details.
In names variable of resultsROI*.mat, I found only 140 ROIs, which
should be 142 ROIs from the neuromorphometrics atlas while
inputting the atlas file you provided in the CONN toolbox.
Two ROIs, including the Left Inferior Lateral Ventricle and Left Optic Chiasm, are not on the list now.
I also checked Setup -> ROIs -> NeuroMorphometrics Atlas
It looks like most ROIs are located in the proper locations.
I can find the Right Inferior Lateral Ventricle and Right Optic Chiasm, but not the contralateral ROIs.
I don't need these 2 ROIs, but I'm wondering if the CONN toolbox ignores tiny ROIs or ROIs outside the brain silhouette.
Best regards,
Chih-Hao Lien
Hi Chih-Hao Lien,
You are right, CONN will disregard specific ROIs if they fall entirely outside of the brain for some subject(s), so I imagine that could perhaps be causing the missing ROIs in your case?.
Best
Alfonso
Originally posted by Chihhao Lien:
Hi Alfonso,
I checked my problem again, and I'd like to provide more details.
In names variable of resultsROI*.mat, I found only 140 ROIs, which should be 142 ROIs from the neuromorphometrics atlas while inputting the atlas file you provided in the CONN toolbox.
Two ROIs, including the Left Inferior Lateral Ventricle and Left Optic Chiasm, are not on the list now.
I also checked Setup -> ROIs -> NeuroMorphometrics Atlas
It looks like most ROIs are located in the proper locations.
I can find the Right Inferior Lateral Ventricle and Right Optic Chiasm, but not the contralateral ROIs.
I don't need these 2 ROIs, but I'm wondering if the CONN toolbox ignores tiny ROIs or ROIs outside the brain silhouette.
Best regards,
Chih-Hao Lien