4 Apr
2022
4 Apr
'22
12:57 p.m.
autorecon1 will not create the white surface, you'll need to do at least autorecon2 or try adding --no-surfs to the tkregisterfv command lien
On 4/4/2022 11:12 AM, Isabelle Deschamps wrote:
External Email - Use Caution
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 "$i"_FS
end
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Monday, April 4, 2022 at 10:56 *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Tkregister2 not opening GUI
*CAUTION:* This email originated from outside of Georgian College. Do not click links or open attachments unless you recognize the sender and know the content is safe.
That recon-all command does not actually do anything. You need to add a directive, eg, -all to do everything. You did not run it even as far as doing the talairach reg, so you can't check it yet. Why not just run everything and to the checks when it is done?
On 4/4/2022 10:11 AM, Isabelle Deschamps wrote:
* External Email - Use Caution * Good morning, Just to follow-up, on this thread. I have permission to read and write. The lh.white does not exist as I have only ran the recon-all -i /Volumes/CopyPaste/fMRI/fMRI/Freesurfer/"$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> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Date: *Sunday, March 27, 2022 at 16:59 *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto: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.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu><freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Date: *Thursday, March 17, 2022 at 22:51 *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu><freesurfer@nmr.mgh.harvard.edu> <mailto: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.edu <mailto: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 <mailto: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 <mailto: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. 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