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To create rReslice_Combined_roi_meanRD.nii, I extracted ROIs from the AAL atlas to code the lesion map by frequency.
Could I use fsaverage for the anatomical reference?
So far, I have: mri_vol2surf --src rReslice_Combined_roi_meanRD.nii --out rReslice_Combined_roi_meanRD_surf.nii --hemi lhrh --out_type nii --regheader /usr/home/register.dat
Which seems to pull the incorrect registration file. Do I need to recreate the registration file with MNI?
Thank you very much – I admit I’m not well versed with coding, trying to learn!
From: Douglas N. Grevemailto:dgreve@mgh.harvard.edu Sent: July 10, 2022 6:11 PM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: How to project SPM image
First, what is rReslice_Combined_roi_meanRD.nii? How was it created? If that is you lesion map, then it is not the right input to BBR. I can't remember, but if the AAL is in the MNI152 space, then it will be easier to just run recon-all on the MNI152 ( or whatever the atnatomical reference is for the AAL). You can then just run mri_vol2surf using --regheader and skip BBR. You may have to play with some of the options (eg, projection fraction)
On 7/5/2022 2:08 PM, Rachel Wagner wrote:
External Email - Use Caution Hello Dr. Greve,
I hope this finds you well! I am currently working on displaying my SPM overlay on a 3D brain volume in FreeSurfer (email below). Dr. Fischl mentioned you may know the command line to do so – I hope this isn’t a bother, I know you must be quite busy – totally understood if you don’t have the time.
So far, I have the following: bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay --s fsaverage \ --init-rr --lta register.lta
I am hoping to smooth out the surface and change the coloring to ultimately export a heatmap image from FreeSurfer that looks something like this.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
Would you have any suggestions for how I should alter my code?
Thank you very much in advance – no problem again if you don’t have the time!
Kind Regards, Rachel Wagner
From: Fischl, Brucemailto:BFISCHL@mgh.harvard.edu Sent: July 5, 2022 9:34 AM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to project SPM image
Hi Rachel
I’ll leave bbreg command lines to others (Doug?), but in general you don’t want to base the registration on the inflated since it doesn’t have a meaningful location within the volume. I would use the standard bbreg command, then use mri_vol2surf to paint what you want onto the surface. Once it is on any surface for a subject you should be able to display it on any other surface for that same subject (and same hemisphere). Cheers Bruce
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: Tuesday, July 5, 2022 12:17 AM 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, that would work very well! I’m trying this code without success, am I missing a component to display on an inflated surface?
bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay --s fsaverage \ --init-rr --lta register.lta
From: Fischl, Brucemailto:BFISCHL@MGH.HARVARD.EDU Sent: July 4, 2022 3:45 PM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to project SPM image
Well you can display it on inflated surfaces instead of white ones, which will remove most of the folds. Then you can smooth the surface overlay however you like (the colors on the surface) in freeview
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: Monday, July 4, 2022 3:27 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, 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.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 7:41 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 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/1NkkNzfSF0MdxMB72IbdKCYeZg06aGs8gUhhlJWAhwEX-z-...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 :)
