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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:
External Email - Use Caution 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Isabelle Deschamps Isabelle.Deschamps@georgiancollege.camailto:Isabelle.Deschamps@georgiancollege.ca Date: Wednesday, 16 March 2022 at 19:20 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.camailto:Isabelle.Deschamps@GeorgianCollege.ca Date: Thursday, March 10, 2022 at 14:52 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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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