I did try tkregisterfv, but I get the following error:

cannot find /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white

[MacBook-Pro-4:~] Isa% tkregisterfv --fstal --s S0010_FS

According to the tutorial, if I leave the –surfs out, the command should work but it does not.

I also tried running it with the –surf I get the same error.

I have only ran the following commands so far:

foreach i ("S0010" "S0028" "S0039" "S0057" "S0074" "S0081" "S0096" "S0120" "S0131" "S0139" "S0146" "S0152" "S0163" "S0168" "S0171" "S0179" "S0205" "S0250" "S0262" "S0263" "S0272" "S0299" "S0300" "S0313" "S0328" "S0363" "S0372" "S0375" "S0378" "S0391" "S0409" "S0418" "S0419" "S0432" "S0442" "S0448" "S0451" "S0471" "S0481" "S0493" "S0504" "S0509" "S0524" "S0525" "S0528" "S0537" "S0544" "S0557" "S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715" "S0727" "S0738" "S0741" "S0747" "S0762" "S0768" "S0770" "S0800" "S0809" "S0837" "S0839" "S0861" "S0888" "S0896" "S0933" "S0949" "S0955" "S0982" "S0988" "S1031" "S1058" "S1082" "S1088" "S1091" "S1128" "S1133")

recon-all -i /Volumes/CopyPaste/fMRI/fMRI/Freesurfer/"$i".anat.nii.gz -subjid "$i"_FS

end

I wanted to verify the registration at this point, but I can.

Thank you for your help,

isabelle

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Date: Thursday, March 17, 2022 at 22:51
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tkregister2 not opening GUI

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Can you try tkregisterfv ? The old tk tools are not supported any more. tkregisterfv uses freeview

On 3/17/2022 6:03 AM, Nathan Kindred (PGR) wrote:

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Hi Isabelle,

It’s been a couple of years since I ran FreeSurfer on a Mac, but I also have had this issue before and it was due to the macOS. I don’t know if anything has changed recently but if not then the only solution would be to try to install an older macOS that will support 32bit apps.

Best,

Nathan

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Isabelle Deschamps <Isabelle.Deschamps@georgiancollege.ca>
Date: Wednesday, 16 March 2022 at 19:20
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FW: Tkregister2 not opening GUI

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Good afternoon,

I am following up on my question regarding the GUI for TKregister2 and TKregister2_Cmld not opening.

Is there another way to open the GUI?

Thank you kindly for your help,

isabelle

From: Isabelle Deschamps <Isabelle.Deschamps@GeorgianCollege.ca>
Date: Thursday, March 10, 2022 at 14:52
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Tkregister2 not opening GUI

Good afternoon,

I am trying to verify the registration and for some reason the GUI is not opening.

I am using a Macbook Pro running macOS Montery with a 2.4 Gz Quad-Core Intel Core i5

I have Freesurfer version: maOS-7.2.0

I do not get an error when I run TKregister2 or TKregister_cmld

This is the output that I get without the GUI opening

No target volume specified, assuming FreeSurfer orig volume.

target  volume orig

movable volume (null)

reg file     (null)

LoadVol   0

ZeroCRAS     1

7.2.0

Diagnostic Level -1

% % % % % % % % avi2talxfm

talairach.xfm ---------------------

1.00857   0.02020  -0.00990  -0.12365;

-0.01789   1.03251   0.24795  -28.10577;

0.02556  -0.30660   1.20913   3.54973;< /span>

0.00000   0.00000   0.00000   1.00000;

INFO: loading target /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/mri/orig.mgz

Zeroing CRAS of target

new xfm -----------------

1.00857   0.02020  -0.00990   1.93629;< /span>

-0.01789   1.03251   0.24795  -11.46406;

0.02556  -0.30660   1.20913  -50.28331;

0.00000   0.00000   0.00000   1.00000;

---------------------

Ttarg: --------------------

-1.00000   0.00000   0.00000   128.00000;

-0.00000   0.00000   1.00000  -128.00000;

0.00000  -1.00000   0.00000   128.00000;

0.00000   0.00000   0.00000   1.00000;

INFO: loading movable /Applications/freesurfer/7.2.0/average/mni305.cor.mgz

Tmov: --------------------

-1.00000   0.00000   0.00000   128.00000;

0.00000   0.00000   1.00000  -128.00000;

0.00000  -1.00000   0.00000   128.00000;

0.00000   0.00000   0.00000   1.00000;

mkheaderreg = 0, float2int = 0

---- Input registration matrix --------

1.00857   0.02020  -0.00990   1.93629;< /span>

-0.01789   1.03251   0.24795  -11.46406;

0.02556  -0.30660   1.20913  -50.28331;

0.00000   0.00000   0.00000   1.00000;

Determinant 1.33659

subject = S0010_FS

RegMat ---------------------------

1.00857   0.02020  -0.00990   1.93629;< /span>

-0.01789   1.03251   0.24795  -11.46406;

0.02556  -0.30660   1.20913  -50.28331;

0.00000   0.00000   0.00000   1.00000;

UnZeroing CRAS for fstal output xfm

Any help would be greatly appreciated.

Isabelle
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