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yunshiuan / label4MRI

Label the brain MNI coordinate by AAL/BA system
GNU General Public License v3.0
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label4MRI in other atlases #12

Open marivas-MRI opened 3 years ago

marivas-MRI commented 3 years ago

Dear label4MRI devs,

First of all congratulations for this useful Toolbox. It is possible to use it with other different atlases than aal? I would like to try with the JHU White Matter atlas.

Thanks in advance.

Best regards,

yunshiuan commented 3 years ago

Currently, both AAL and Brodmamn templates are supported. Adding the support for other atlases is certainly possible. Please name the atlases that you are considering and I will include them in the next update.

marivas-MRI commented 3 years ago

Thank you! I am considering to use the JHU-WhiteMatter (1mm) atlas included in MRICron. You can find in attached the nii file as well as the labels.

JHU-WhiteMatter-labels-1mm.nii.gz JHU-WhiteMatter-labels-1mm.nii.txt

yunshiuan commented 3 years ago

Noted. I will include it in the next update.

marivas-MRI commented 3 years ago

Dear Chuang,

Instead of using the JHU atlas version included in MRICron that I sent to you in my previous message, can you implement in label4MRI package this version of the JHU atlas that is included in FSL? You can find in attached the atlas as well as the txt file with the labels.

Excuse me for this last change and thank you so much in advance!.

Best regards,

JHU-ICBM-labels-1mm.nii.gz JHU-WhiteMatter-labels-1mm.nii.txt

yunshiuan commented 3 years ago

Noted. They are added to my to-do list.

signehagner commented 2 years ago

Dear Yunshiuan,

Has this feature with other atlases been implemented yet? Thank you for a great tool!

All the best, Signe

PHJT003 commented 5 months ago

Dear @yunshiuan, would it be possible to add the Harvard-Oxford template of MRIcron?

I am also wondering how one would go about implementing an atlas in label4MRI. Is there any resource I can check out?

Thank you so much.

All the best, Valerio

yunshiuan commented 4 months ago

Hi @signehagner @PHJT003 sorry for the delay. It should be very straightforward. I would appreciate if you are willing to create an PR had you added the template.

All templates are supposed to be stored in https://github.com/yunshiuan/label4MRI/blob/master/data-raw/label4mri_metadata.R and https://github.com/yunshiuan/label4MRI/blob/master/data-raw/metadata.RData

PHJT003 commented 4 months ago

Hi @yunshiuan, thanks for your reply. I forked your repo, inspected the .R files you pointed to, and tried to implement the Harvard-Oxford (HO) atlas.

I retrieved the HO atlas from the ~\Resources\templates folder of MRIcron. However, while the AAL atlas is stored as a simple text file, the HO one is saved with a .nii.gz extension: HarvardOxford-cort-maxprob-thr0-1mm.nii.gz.

I tried to extract the file and open it in R but had no success with it. Maybe I am missing something basic here, but I am stuck. If you or anyone else in the thread have any pointers to get past this impasse, I would appreciate them very much.

Thanks, Valerio

marivas-MRI commented 1 month ago

Hi,

Is available a label4MRI version that includes the JHU atlas?

Thank you.