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>
Sent: Friday, January 19, 2024 10:08 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
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
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1Jks6aGDbVRK45MXX_bng2dSYKT5jA6CUTif0iwWA4-fH6rTRJM4W1Oxzl4j1l9u-hH14NMZLdVW4hCVVvKKtbqJeubr8HH2gBo5awdxomjWFcVxXiX1udEhpl-NGWubyRT80xfkBm6ym6mujJMMD9VkrKOG2f1EPd1krkFnE04TfdwkocdEwT0y4iO17c2x3HkoAs0NbtXvP9lgYhrWwu5geMpe6ALH3HS5BGIGerTBWwurZlwG-u86DMShAQroAWsCMWufjSPB0OLtmEa7wRBfFdkc-6qJ8dhFogg0frmDKENTGczvMwM3WibDMUwLj/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
