Can you give us more details? How did you create the
rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are you trying
to display it? On an average surface? Why are you mapping it to bert and not
fsaverage?
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 6:26 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image
External Email - Use Caution
Hello Dr. Fischl, thank you for your reply, it is much appreciated.
I am trying to cortically project my spm lesion location/frequency map,
according to instructions linked here: AnalyzingData/MNE_SPM2Freesurfer - Meg
Wiki
(cam.ac.uk)<https://secure-web.cisco.com/1Qq-eLDAcZvkiA1oj8V5IkWowioqEfn5og-amJx-SY4k1in27LFW-IYPjtKPBkz1pSyyypTf849rJVAmyJ-Xzl8hgSfRw_PnCU1IcK9vgJzylh5b5zbo__pkcMlQw3COQCtiD9Sjb3UUrTitRCZHp7K2aER3VxlzHcdNjLpvYNT25_gZPm3q08d1C6zm3oJAaOEzRs2pM7XWXRyfFr4kIvENC6HRC5Rym2tl9beh-v6o3WhIxUvTxUqG9UKik41wBeLCBHAlxXgQSjetU13wcX3LQV4OqWruZLoxxbjFjgttUeagi7QRPA8pJi6cegsKrkFGhnEdEFvpjRnL8d5vHBg/https%3A%2F%2Fimaging.mrc-cbu.cam.ac.uk%2Fmeg%2FAnalyzingData%2FMNE_SPM2Freesurfer>
I have used the following code: bbregister --mov
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta
register.lta
However, my results still look very grainy. Is there a better way to do this?
Thank you again,
Rachel Wagner
From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: June 30, 2022 9:09 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image
Can you summarize what you are trying to do? What kind of overlay are you
trying to visualize and what exactly do you mean by a "3D image"?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image
External Email - Use Caution
Thank you so much for your response - I'm a master's student and am really
struggling - I've been stuck trying to do this for about 2 weeks now, so the
help is so appreciated!
My results look very grainy in mricron so my supervisor wants me to keep trying
in FreeSurfer unfortunately for me.
I uploaded a the brain.mgz volume in freeview, but I'm not sure how to add an
overlay and project as a 3D image. Would you happen to have any ideas?
Thank you so, so much again,
Rachel Wagner
From: niels.f...@gmx.de<mailto:niels.f...@gmx.de>
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image
You don't often get email from niels.f...@gmx.de<mailto:niels.f...@gmx.de>.
Learn why this is
important<https://secure-web.cisco.com/1IGyjHfcGxatghbnnU4QrmkjiCFhtGpKgDShLha5LYdEXD8WHfidRqqVti-tRNc_NRrmceKvWCQqvppztwIyjyHoLtCRG8g-_oV0axWfVJBREqBDdqXiWbD3r4lqXwu1ATUnSHzr1Sm0hzwo9fZKMmaip9vMaZ-ziZtyq-o7jLLqcFSCJKMqj--KkVlWH1krwZu6xMc3iky_sPV5EDDuis16g4Bsx9Gtgx_ok2cbVmfCOgmv9kF1iV6S_H9cshZy0_0U2pGRX1vhHUDPzaaKSiDD2oKm3dVcgmx1rmzjlgOP78SWxfDc_SlHhotPQ8vOpc-kxEyf5XH9hCJY2HviLIg/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>
Sure is, through freeview, however if you already have spm format files, it is
much easier to use mricron
Von:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Im Auftrag von Rachel Wagner
Gesendet: Donnerstag, 30. Juni 2022 18:18
An: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] How to project SPM image
External Email - Use Caution
Thanks very much, I will absolutely do so! Just so I know - is there not any
way of generating such figures in Freesurfer?
From: niels.f...@gmx.de<mailto:niels.f...@gmx.de>
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image
You don't often get email from niels.f...@gmx.de<mailto:niels.f...@gmx.de>.
Learn why this is
important<https://secure-web.cisco.com/1i1UJeVjwlumrCAM-yAFlTcIKRz-AyoK3nEvXbthMrwntcUHURlFyX0rrFR0wouQHmspA4ZjoxOBIENpbDQzxXHDKpH2XTzH9AVcV2-B4cB0UnhepvutfJUWDgE0-b-jVluP0RVxcQb-6AbvjsVgjiH9THZp_5rNkZbCuvXkXkry7ESkyYXR4FggRrHhNYLoaEY5HgYqZwH5KsROiIvUMmu53rbttVpblAHaQUYBctJJR9xT50C6dDBPznLTYAWAisLm9sL6xcef1unrvAi6o59VwqbVaOLCnJmSHsjZ0sV9dPYEKoTc4lyh75EVhpn0SIbo5FCH1IrROZqKSf0rP1g/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>
External Email - Use Caution
Rachel, these figures were likely created with a software called mricron, not
freesurfer. Check it out :)
Holen Sie sich Outlook für
Android<https://secure-web.cisco.com/1XvY3sA4-dRCvGWfgKiNWJHfOTGrrzAnDZB_-8JrFkF7ZCfI9UW5jD-mM3a0HD6u6u-XOhrGWWBIWdw7cY7iSa6VTZTpj5EPSIccAc83wMVuyE_Chh-Y41UAN1BN5hQgeEgwVxgy85ZFxD7a8RVjtO8x6YqLzn7R9EMm2j7-fuhi78CfCs8nGC2FCMTkxO59TfxCqAzZqBqbxZZYQSG8lgqX6_TrMa4UUKSK6XvwvVg2tbqUcsVxSl7jUvScAgBwcwlyfhyTurS387OW-PVJF9KA3zrYsboQDmxhlaGQRAaebLvS6Y_IpKv4NbRNQeNiKP1WYwTYcY_qpo0Wyl9Kxkw/https%3A%2F%2Faka.ms%2FAAb9ysg>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
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.
