External Email - Use Caution
Please disregard previous email! I was able to run recon-all on the
MNI template and named it template_RW.nii
I have run the following code:
mri_vol2surf --src rReslice_Combined_roi_meanRD.nii --regheader
template_RW.nii --projfrac 0.5 --hemi lh --out /home/developer/template
And am getting this error:
srcvol = rReslice_Combined_roi_meanRD.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /home/developer/template/template_RW.nii/mri/orig.mgz as
target reference.
error: mghRead(/home/developer/template/template_RW.nii/mri/orig.mgz,
-1): could not open file
Am I setting the registration incorrectly?
Thank you again!
Rachel
*From: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent: *July 10, 2022 6:11 PM
*To: *Freesurfer support list <mailto: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, Bruce <mailto:bfis...@mgh.harvard.edu>
*Sent: *July 5, 2022 9:34 AM
*To: *Freesurfer support list <mailto: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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@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.edu>
<mailto: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, Bruce <mailto:bfis...@mgh.harvard.edu>
*Sent: *July 4, 2022 3:45 PM
*To: *Freesurfer support list <mailto: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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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.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, Bruce <mailto:bfis...@mgh.harvard.edu>
*Sent: *July 3, 2022 7:44 PM
*To: *Freesurfer support list <mailto: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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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://drive.google.com/file/d/150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD/view?usp=sharing
<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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl,
Bruce <bfis...@mgh.harvard.edu>
*Sent:* Sunday, July 3, 2022 6:37:42 PM
*To:* Freesurfer support list <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-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
<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>
*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
*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
*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>
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