Re: [Freesurfer] Freeview GUI overlay and registration

[Douglas N. Greve]

On 6/15/2022 1:26 PM, Kuo, Yi-Ling wrote:


Hello,

The below solutions sounded like data need to be analyzed with 
Freesurfer individually to get the registration file?


The anatomical  must be analyzed in FS, but not the fMRI. See eg 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview


I realized that the stats can be presented in Freeview with the 
correct locations in T1, but when it comes to inflated surface, the 
BOLD signals always present in a specific location regardless of 
dataset (please see the attached figure, looks like it’s a 
registration issue). I wonder if the data were already analyzed by FSL 
in group level, is it possible to present the analyzed group data on 
inflated surface in Freeview?



Yes, see web page above


Thank you again for helping,

Irene

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Date: *Wednesday, June 8, 2022 at 11:15 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Freeview GUI overlay and registration

You will need an lta file that maps from the anatomical to the fmri. 
You can get this with something

bbregister --mov template.nii.gz --s subject --t2 --reg reg.lta
where template.nii.gz is the fmri motion correction template or the 
mean fmri (I forgot what it is called in FSL)


On 6/3/2022 5:12 PM, Kuo, Yi-Ling wrote:

Hi Freesurfer experts,

I am trying to use the Freeview GUI to load fMRI BOLD activation
data (analyzed in FSL) and project on the inflated surface. I used
the feature “Overlay/Load generic” and was prompted to select
overlay file and/or apply registration. The selected overlay file
didn’t seem to project on the right spot on the inflated surface
as would be seen in T1. If registration was the issue, what
registration file should be selected in the Freeview GUI?

My Freeview was updated. Thank you very much for helping.

Irene



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Re: [Freesurfer] Freeview GUI overlay and registration

[Douglas N. Greve]

You will need an lta file that maps from the anatomical to the fmri. You 
can get this with something

bbregister --mov template.nii.gz --s subject --t2 --reg reg.lta
where template.nii.gz is the fmri motion correction template or the mean 
fmri (I forgot what it is called in FSL)


On 6/3/2022 5:12 PM, Kuo, Yi-Ling wrote:


Hi Freesurfer experts,

I am trying to use the Freeview GUI to load fMRI BOLD activation data 
(analyzed in FSL) and project on the inflated surface. I used the 
feature “Overlay/Load generic” and was prompted to select overlay file 
and/or apply registration. The selected overlay file didn’t seem to 
project on the right spot on the inflated surface as would be seen in 
T1. If registration was the issue, what registration file should be 
selected in the Freeview GUI?


My Freeview was updated. Thank you very much for helping.

Irene


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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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[Freesurfer] Freeview GUI overlay and registration

[Kuo, Yi-Ling]

Hi Freesurfer experts,

I am trying to use the Freeview GUI to load fMRI BOLD activation data (analyzed 
in FSL) and project on the inflated surface. I used the feature “Overlay/Load 
generic” and was prompted to select overlay file and/or apply registration. The 
selected overlay file didn’t seem to project on the right spot on the inflated 
surface as would be seen in T1. If registration was the issue, what 
registration file should be selected in the Freeview GUI?

My Freeview was updated. Thank you very much for helping.

Irene
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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 believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.