External Email - Use Caution
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:
External Email - Use Caution 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Thursday, March 17, 2022 at 22:51 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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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