[Freesurfer] Export Image

External Email - Use Caution Hello everyone, this is probably a silly question, but how can I export images from freeview? I don’t see an export option! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] How to project SPM image

esults 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

Re: [Freesurfer] How to project SPM image

isplay it? On an average surface? Why are you mapping it to bert and not fsaverage? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rachel Wagner Sent: Sunday, July 3, 2022 6:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] How to project SPM image External Email - Use C

Re: [Freesurfer] How to project SPM image

he 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nm

Re: [Freesurfer] Command Not Found

l, Are you trying to run tkregister2? Looks like you forgot the t at the start of the command. -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Rachel Wagner Sent: Tuesday, June 28, 2022 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Command Not Found

[Freesurfer] Cortical Projection

External Email - Use Caution Hello all, I am currently working on displaying my SPM overlay on a 3D brain volume, using bbregister, and am getting this:

Re: [Freesurfer] Tksurfer Error

:33 PM, Rachel Wagner wrote: External Email - Use Caution Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg register.dat And got this error: Tcl_Init failed: Can't find

Re: [Freesurfer] FW: How to project SPM image

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 (emai

Re: [Freesurfer] FW: How to project SPM image

ave 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. Fisc

[Freesurfer] mri_vol2surf error

External Email - Use Caution Hello everyone, I am trying to display my lesion map I created in Matlab on a cortical surface, and am getting the following error: developer@developer-VirtualBox:~$ mri_vol2surf --mov rReslice_Combined_roi_meanRD.nii --mni152reg --trgsubject

[Freesurfer] Command Not Found

not found Is my path not set correctly? Thanks again, Rachel Wagner ___ 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

[Freesurfer] How to project SPM image

21z-g7X2quN2TvlfuFTh8yU4nUstoua4zkPO1Jx8NGEU54Z5srWhovYcnGhXjxKA3oZnHQ31KZzxIyTw/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41591-022-01834-y%2Ffigures%2F4> Has anyone done this before and would be able to point me towards any resources to do so? Thank you, Rachel

[Freesurfer] Tksurfer Error

External Email - Use Caution Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg register.dat And got this error: Tcl_Init failed: Can't find a usable init.tcl

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

Re: [Freesurfer] How to project SPM image

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

Re: [Freesurfer] How to project SPM image

nd, 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 On Behalf Of Rachel Wagner Sent: Tue

Re: [Freesurfer] How to project SPM image

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 On Behalf Of Rachel Wagner Sent: Monday, July 4, 2022 3:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] How to

[Freesurfer] SPM to FreeSurfer

External Email - Use Caution Hello, I am trying to take my SPM images and cortically project them with free surfer (SpmPainting - Free Surfer Wiki

Re: [Freesurfer] FSL Password

:08 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Rachel Wagner<mailto:rwag...@uwo.ca> Subject: Re: [Freesurfer] FSL Password You don't often get email from fsbu...@contbay.com. Learn why this is important<https://secure-web.cisc

Re: [Freesurfer] SPM to FreeSurfer

): could not open file developer@developer-VirtualBox:~$ From: Rachel Wagner<mailto:rwag...@uwo.ca> Sent: June 15, 2022 5:04 PM To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> Subject: SPM to FreeSurfer Hello, I am trying to take my SPM images and cortically

[Freesurfer] Nii to Img file

External Email - Use Caution Hello, Thank you for your assistance! I am trying to convert an nii nifti file to an img file within free surfer. I’ve used the mri convert function and did create the img file, but I’m getting an error message in SPM when I try to co-register it

[Freesurfer] FSL Password

External Email - Use Caution Hello, I am downloading FSL into ubuntu freesurfer VM, and have gotten the following prompt: developer@developer-VirtualBox:~/Downloads$ python3 fslinstaller.py --- FSL Installer - Version 3.2.3 --- [Warning] Some operations of the installer

[Freesurfer] Setting Location?

from Combined_roi_meanRD.nii... error: niiRead(): error opening file /home/developer/Combined_roi_meanRD.nii I believe this is due to the location I have stored it (desktop); how do I set the location? Thank you, Rachel Wagner ___ Freesurfer mailing list

[Freesurfer] Image Edits

, 0.2, 0.3...1? Even when selecting the ‘fixed axis’ option, it seems to automatically adjust. Thanks! Rachel Wagner ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] Error Opening File

External Email - Use Caution Hello, I am getting the following error when trying to convert a file on my desktop: developer@developer-VirtualBox:~$ mri_convert home/developer/desktop/brain.mgz brain.nii mri_convert home/developer/desktop/brain.mgz brain.nii reading from

[Freesurfer] Converting File Type

External Email - Use Caution Hello, I have an img and an mgz file I would like to convert to a nii file. How can I do so? Thanks! Rachel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Unsupported Datatype

mr.mgh.harvard.edu>> On Behalf Of Rachel Wagner Sent: Tuesday, November 15, 2022 11:23 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Unsupported Datatype External Email - Use Caution Hello, I’m getting the following error, not s

[Freesurfer] Unsupported Datatype

-t2_swi_tra_p2_3mm_Mag.nii Thanks! Rachel Wagner ___ 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

[Freesurfer] (no subject)

External Email - Use Caution Please unsubscribe me ___ 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

[Freesurfer] Directory not set properly?

-I_RCMVVFJSmzLFKTkiHNx6WEcVs17okJNyj5sNVboDUvLakOmQnm3HGpsbVZedgB5-kPvzkr9XNg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting developer@developer-VirtualBox:~/freesurfer$ Is it that my path is not set correctly? Thank you! Rachel Wagner ___ Freesurfer mailing list Freesurfer

[Freesurfer] Ubuntu compatibility

External Email - Use Caution Hello, I am trying to use mri_easyreg on Ubuntu 18 and realize I need to upgrade to freesurfer 7.3.2 to use this function. I am encountering issues downloading 7.3.2. Are the two compatible? Is there a link for setup I should follow? Thanks,

[Freesurfer] Code not working

External Email - Use Caution Hello all, I’m getting an error as follows: developer@developer-VirtualBox:~/freesurfer$ setenv SUBJECTS_DIR $FREESURFER_HOME/subjects Command 'setenv' not found, did you mean: command 'getenv' from snap getenv (0.3.1) See 'snap info ' for

[Freesurfer] Unable to read in images from Freeview command window

/lh.white:edgecolor=red error: mghRead(/home/developer/freesurfer/004/mri/wm.mgz, -1): could not open file MRIread failed: Unable to read from /home/developer/freesurfer/004/mri/wm.mgz I don’t know how to resolve this, any guidance would be greatly appreciated. Thank you, Rachel Wagner

[Freesurfer] Command not found

-VirtualBox:~/freesurfer$ freeview Command 'freeview' not found, did you mean: command 'treeview' from deb treeview Try: sudo apt install Is there any way to resolve this? Thanks, Rachel Wagner ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu