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.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:
* 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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Isabelle Deschamps <Isabelle.Deschamps@georgiancollege.ca> <mailto:Isabelle.Deschamps@georgiancollege.ca> *Date: *Wednesday, 16 March 2022 at 19:20 *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:Isabelle.Deschamps@GeorgianCollege.ca> *Date: *Thursday, March 10, 2022 at 14:52 *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto: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. targetvolume orig movable volume (null) reg file(null) LoadVol0 ZeroCRAS1 7.2.0 Diagnostic Level -1 % % % % % % % % avi2talxfm talairach.xfm --------------------- 1.008570.02020-0.00990-0.12365; -0.017891.032510.24795-28.10577; 0.02556-0.306601.209133.54973;< /span> 0.000000.000000.000001.00000; INFO: loading target /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/mri/orig.mgz Zeroing CRAS of target new xfm ----------------- 1.008570.02020-0.009901.93629;< /span> -0.017891.032510.24795-11.46406; 0.02556-0.306601.20913-50.28331; 0.000000.000000.000001.00000; --------------------- Ttarg: -------------------- -1.000000.000000.00000128.00000; -0.000000.000001.00000-128.00000; 0.00000-1.000000.00000128.00000; 0.000000.000000.000001.00000; INFO: loading movable /Applications/freesurfer/7.2.0/average/mni305.cor.mgz Tmov: -------------------- -1.000000.000000.00000128.00000; 0.000000.000001.00000-128.00000; 0.00000-1.000000.00000128.00000; 0.000000.000000.000001.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.008570.02020-0.009901.93629;< /span> -0.017891.032510.24795-11.46406; 0.02556-0.306601.20913-50.28331; 0.000000.000000.000001.00000; Determinant 1.33659 subject = S0010_FS RegMat --------------------------- 1.008570.02020-0.009901.93629;< /span> -0.017891.032510.24795-11.46406; 0.02556-0.306601.20913-50.28331; 0.000000.000000.000001.00000; UnZeroing CRAS for fstal output xfm Any help would be greatly appreciated. Isabelle _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1zaeF4vWqmYPaEGHriGOdX-rtQfn5wV_msTWvwktKdsjsMBvxbcei-uwdk2G07NUWubscVJq_2YaWQtTgSMIxd-mlmb0QEvl6lFEqOLEeVLdWKe7pDSWzJ19uDB716dQbm3-vK6dlkTyjIb-qzlSfiXEY-am4SqrMEKMKqZ392-oJbaa0wgzX0j0_bSzJohLh5oQvKKbBQri4sposjS_y51imfcJ23FKQWI_YGvGR4rMBVSCisZ4N8njHt8Y07DdZou0T822xO8jV983FsJmCxvkYl-BXCn9pu_4a2uG9N7idueUnLu289qzWVhUlyhQfpxuS8OPnE_ke3tZlEKWtcA/https%3A%2F%2Fcan01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cisabelle.deschamps%2540georgiancollege.ca%257Cb6bf297cad544fc1032808da088a34ba%257Cda9a94b6468149bcbd7cbab9eac0ad3c%257C0%257C0%257C637831686943803579%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DOs7osdxgIivZCDgUPbEMq1YgQhDg69xas%252Bv38%252BZVN0I%253D%26reserved%3D0>
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