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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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, Brucemailto:BFISCHL@mgh.harvard.edu Sent: June 30, 2022 9:09 PM To: Freesurfer support listmailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.foit@gmx.demailto:niels.foit@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.foit@gmx.demailto:niels.foit@gmx.de. Learn why this is importanthttps://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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Rachel Wagner Gesendet: Donnerstag, 30. Juni 2022 18:18 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.foit@gmx.demailto:niels.foit@gmx.de Sent: June 30, 2022 4:47 AM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to project SPM image
You don't often get email from niels.foit@gmx.demailto:niels.foit@gmx.de. Learn why this is importanthttps://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 :)