Hi Anna
The DK atlas (or DKT?) gets written into the aparc+aseg.mgz volume, but the DKT parts of it only consist of cortex. The subcortical labels are the normal ones (caudate, putamen, etc...)
Cheers Bruce
From: Arkhipova Anna, MUDr. Anna.Arkhipova@fnol.cz Sent: Monday, January 29, 2024 10:21 AM To: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu; Freesurfer@nmr.mgh.harvard.edu; fischl fischl@nmr.mgh.harvard.edu Cc: phlustik@upol.cz; Jasenská Monika, Ing. Monika.Jasenska@fnol.cz Subject: Re: conversion of D-K atlas
External Email - Use Caution Hello Bruce,
Thank you very much for helping us.
Basically, we would like to replicate the methodology of Poudel 2021, the study I sent to you in the last email.
If you can have a look at Figure2 in the paper: we are now at the step (ii) and we need to apply the D-K atlas (including the subcortical regions) to the parcellation of our fMRI data. This step should extract BOLD time-courses from 82 regions "as per DK atlas".
Since finding the D-K atlas (in 3D space as a Nifti file) through other authors wasn't succeeded, we were trying to convert the D-K atlas from Freesurfer to Nifti file ourselves.
Then, in order to run recon-all, as you have suggested, a member of our team found and tried the command I copied in the last email, but we are not sure if it was the right one, because we see the name Talairah (see screenshot, on the right bottom).
I hope my explanation makes sense to you.
Best regards, Anna
________________________________ From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: January 19, 2024 4:17:43 PM To: Arkhipova Anna, MUDr.; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu; fischl Cc: phlustik@upol.czmailto:phlustik@upol.cz; Jasenská Monika, Ing. Subject: RE: conversion of D-K atlas
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Maybe you can give us more details about what you are trying to do? Generate an fMRI time-series that is the average response in each cortical parcel? And subcortical structure? The subcortical segmentation is not Talairach, although I'm not sure that is relevant. Generating the average time series should be pretty straightforward if that is what you want (although Doug will know the commands better than I do)
Cheers
Bruce
From: Arkhipova Anna, MUDr. <Anna.Arkhipova@fnol.czmailto:Anna.Arkhipova@fnol.cz> Sent: Friday, January 19, 2024 10:08 AM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu>; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu; fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Cc: phlustik@upol.czmailto:phlustik@upol.cz; Jasenská Monika, Ing. <Monika.Jasenska@fnol.czmailto:Monika.Jasenska@fnol.cz> Subject: Re: conversion of D-K atlas
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Hi Bruce,
thank you a lot for your kind reply.
Unfortunately, we've got further question, since we tried the following command:
recon-all -sd $PWD/surf -all -i ./Mprage.nii.gz -s $PWD -parallel -openmp $num_cores
and acquired a cortical-level parcellation according to the D-K atlas, but the subcortical parcellation was produced (we think) automatically according to the Talairach atlas (see attached).
Actually, we would like to get time-series in 82 brain regions as per D-K atlas, which should generate a vector of size 82x1 according to the methodology of Poudel et al. J Neural Eng. 2021.
However, as you wrote that D-K atlas is only cortical, would you think that it is possible at all (to get cortical + subcortial via D-K)?
Or have we proceeded wrongly?
We are sorry for repeatedly bothering you..
(We have tried to contact for the atlas both prof. Killiany and dr. Desikan, who sadly passed away, and also asked dr. Poudel himself, but he suggested a different atlas (we are not sure why) without subcortical regions.)
Thank you very much again!
Best regards,
Anna and lab team
________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: January 9, 2024 3:48:23 PM To: Arkhipova Anna, MUDr.; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu; fischl Cc: phlustik@upol.czmailto:phlustik@upol.cz Subject: RE: conversion of D-K atlas
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Hi Anna
Parcellation is more than just format conversion - you need to map it onto the details of an individual subject's anatomy. In addition, the DKT atlas is only cortical. If you want subcortical regions in addition you should run recon-all as it will produce both.
Cheers
Bruce
From: Arkhipova Anna, MUDr. <Anna.Arkhipova@fnol.czmailto:Anna.Arkhipova@fnol.cz> Sent: Tuesday, January 9, 2024 6:14 AM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu; fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Cc: phlustik@upol.czmailto:phlustik@upol.cz Subject: conversion of D-K atlas
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Dear prof. Fischl,
We would like to kindly ask a question, if there is a way to convert Fressurfer Atlas Desikan-Killiany (lh and rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs) to Nifti file for parcellation of our resting-state fMRI data.
Although we have tried script mri_convert, we obtained only cortical regions, but we need also subcortical regions. Would it be anyhow possible?
Thank you so much in advance.
Sincerely yours, Anna Arkhipova, MD
fMRI laboratory Department of Neurology, Faculty of Medicine and Dentistry Palacky University and University hospital Olomouc Czech Republic
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