My apologies. I did run autorecon1. I copied the wrong part of the script. Should I just run as you suggested -all and do the edits after? Freeview should open then, as I will have the required files.

isabelle

foreach i ("S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715" "S0727" "S0738")

recon-all -autorecon1 -subjid "$i"_FS

end

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Date: Monday, April 4, 2022 at 10:56
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tkregister2 not opening GUI

CAUTION: This email originated from outside of Georgian College. Do not click links or open attachments unless you recognize the sender and know the content is safe.

That recon-all command does not actually do anything. You need to add a directive, eg, -all to do everything. You did not run it even as far as doing the talairach reg, so you can't check it yet. Why not just run everything and to the checks when it is done?

On 4/4/2022 10:11 AM, Isabelle Deschamps wrote:

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Good morning,

Just to follow-up, on this thread.

I have permission to read and write. The lh.white does not exist as I have only ran the

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

I wanted to verify the registration before moving on to the other stages, and according to the tutorial, this is something that can be done. Do you recommend that are run the rest of the pipeline and then go back and verify registration?

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: Sunday, March 27, 2022 at 16:59
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tkregister2 not opening GUI

CAUTION: This email originated from outside of Georgian College. Do not click links or open attachments unless you recognize the sender and know the content is safe.
Does /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white exist and do you have permission to read it? If yes to both, then try running it with --debug as the first option, then send all the terminal output

On 3/21/2022 5:02 PM, Isabelle Deschamps wrote:
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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

CAUTION: This email originated from outside of Georgian College. Do not click links or open attachments unless you recognize the sender and know the content is safe.
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

⚠ External sender. Take care when opening links or attachments. Do not provide your login details.

        External Email - Use Caution

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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