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Thank you, noted!
I think I am on the right track, but I’d like to smooth the surface out (particularly the coloring and the sulci, which are quite deep) considerably – is there any way for me to do that?
From: Fischl, Brucemailto:BFISCHL@mgh.harvard.edu Sent: July 3, 2022 7:44 PM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to project SPM image
I see, and what’s wrong with the screen shot you have? (and “Bruce” is fine).
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Rachel Wagner Sent: Sunday, July 3, 2022 7:41 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to project SPM image
External Email - Use Caution Hi Dr. Fischl,
My apologies, I don’t have much of a background in software generally!
For the SPM image, I used the AAL atlas to label lesioned brain regions and colored by frequency to generate the heatmap. Image dimensions: 1x1x1, Image Size [91 109 91], Pixel Dimensions [2 2 2], Bits Per Pixel: 32. I will map onto fsaverage!
I’m hoping to display it as a heatmap on an average surface, to look something like this: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be | Decreased functional connectivity from Wernicke's area homologue in... | Download Scientific Diagram (researchgate.net)https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXSkjJ6wTsTr4oavOgdzgC__DuhBfa2YoeXPPAkWNDkDveceWCqonnMePOe7RO8-EzKOCNiY55G6RP0RxIqcSzGoy5xrThG11tzNHAx4J2oOvo_ESpDm-Xy5SRds7mHaMi14AVwz97DtG6A7__AhYWMzxD1DhY1be4RuervQ_3GhIJP9U47Jlyf-6BJDot29n-DzmhaePM1AHaWepGK-h2DLlNNr5gjpR4VuJMYqBEkqYBtAH7eWX7f2lcu_279ka4M5ClsgZa3q8hqXJMfnAB0nP3mVb7RfWqryW2ibpstA/https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FDecreased-functional-connectivity-from-Wernickes-area-homologue-in-children-born-VPT_fig3_329809185
This is a screenshot of what I currently have within FreeSurfer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1W1qPJh0LIQdhLZew9v66ICIq4AvFY0hvWp5vgpcvBdzUKG...https://secure-web.cisco.com/117ePUqDOWTzA8pswn-Mibsr2qBEZIMKV-Yd9P886w1Gz_L53sraXddp6xh_K6otFd1qp6tl3kHUNUk5TqYrNzizCdMJEp5zKR4XRSMj-pTdv0Us9VNWBasmYcsRRwLCrbr56qNZWBqSCMo1n9uuDVn2jwX3TJvflVYJ5eFy_AeuSRsYP4IZpVfIgQa_M_jpxzqEUcOyymM_iHc8lqsaOMkCXyzUnvQHwgy4EzHxKFkCoCHHa5jVAf9Gnol0mf4Yr2C8MosmAo4UiuPBgk6J_IX3DQcx-3NEMfUZdj7TOzoVG7H3Nuaid0CL4spvphW5d5l6r4qJCNk1rNi9tIb_xxQ/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Dsharing
Thank you very much again for your help! Rachel
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 Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Sunday, July 3, 2022 6:37:42 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] How to project SPM image
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.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: Sunday, July 3, 2022 6:26 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] How to project SPM image
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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
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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
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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
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Rachel, these figures were likely created with a software called mricron, not freesurfer. Check it out :)
