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.arkhip...@fnol.cz>
Sent: Monday, January 29, 2024 10:21 AM
To: Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu>;
Freesurfer@nmr.mgh.harvard.edu; fischl <fis...@nmr.mgh.harvard.edu>
Cc: phlus...@upol.cz; Jasenská Monika, Ing. <monika.jasen...@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
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: January 19, 2024 4:17:43 PM
To: Arkhipova Anna, MUDr.;
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl
Cc: phlus...@upol.cz<mailto:phlus...@upol.cz>; Jasenská Monika, Ing.
Subject: RE: conversion of D-K atlas
Upozornění: Tento e-mail přišel z externí e-mailové adresy. Dbejte zvýšené
opatrnosti při otvírání příloh a odkazů v textu mailu, nezadávejte svoje
přihlašovací údaje.
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.arkhip...@fnol.cz<mailto:anna.arkhip...@fnol.cz>>
Sent: Friday, January 19, 2024 10:08 AM
To: Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>;
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
Cc: phlus...@upol.cz<mailto:phlus...@upol.cz>; Jasenská Monika, Ing.
<monika.jasen...@fnol.cz<mailto:monika.jasen...@fnol.cz>>
Subject: Re: conversion of D-K atlas
External Email - Use Caution
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
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: January 9, 2024 3:48:23 PM
To: Arkhipova Anna, MUDr.;
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl
Cc: phlus...@upol.cz<mailto:phlus...@upol.cz>
Subject: RE: conversion of D-K atlas
Upozornění: Tento e-mail přišel z externí e-mailové adresy. Dbejte zvýšené
opatrnosti při otvírání příloh a odkazů v textu mailu, nezadávejte svoje
přihlašovací údaje.
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.arkhip...@fnol.cz<mailto:anna.arkhip...@fnol.cz>>
Sent: Tuesday, January 9, 2024 6:14 AM
To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>;
fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
Cc: phlus...@upol.cz<mailto:phlus...@upol.cz>
Subject: conversion of D-K atlas
External Email - Use Caution
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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