sounds like something is wrong with the image. Did you look at ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a head?
On 5/28/2024 6:07 AM, Chen Yang wrote: > External Email - Use Caution > > Hi everyone, > > I tried to run the reconstruction with the command line: recon-all -i > ANTS_QS_template_MNI.nii.gz -subject CGBT -all > > then I got the error message: > talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > talairach_avi log file is transforms/talairach_avi.log... > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log > Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 > GNU/Linux > > And this is the error message in the talairach_avi.log: > imgrege: no voxels in register > ERROR: 'imgreg_4dfp > /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305 > > /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask > talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! > status=254 > ERROR: mpr2mni305 execution aborted > > Does anyone know how to solve this problem? Thanks so much! > > Best, > Chen > ----- Original Message ----- >> From: "Chen Yang" <ya...@cbs.mpg.de> >> To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >> Sent: Monday, 20 May, 2024 13:59:13 >> Subject: [Freesurfer] Recon-all for a common template > >> External Email - Use Caution >> >> Dear Freesurfer Developers, >> >> my data is from 50 preschoolers and I created my own group template from >> these >> kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file >> (see attached). Then we'd like to process this group template in Freesurfer >> to >> reconstruct the cortical surfaces as the individual brain images. My question >> is, how can i do the recon-all with the template? Because I only have this >> template file I feel I don't have enough input files(?). >> >> Thanks in advance! >> >> Best regards, >> Chen >> >> -- >> Chen Yang >> >> PhD Student >> Independent Research Group 'Milestones of Early Childhood Development' >> Max Planck Institute for Human Cognitive and Brain Sciences >> >> Email:ya...@cbs.mpg.de >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/152_yjWgWiW7QaUCNWdHFdgPDgbGmCDd24wrNL32r-4bja7mb7PwZLrVrT8x_Ot8oLBlBDSrPO5K5UwFJww_c_Y6HNu9vVaziQgviXOWppVzFqlFYr7Go-t0P0ERBoTxsiCjkgkjp8sqNY12lF_6KIfy959AukP9K4eVWkLGWIlqP1lI_TQg2slA5qX1X8cEK857YHHC7vYcLM4qF7sKEU0nJ9xOLxq89J8jkqjRr9_G8fkxbUlriLEANx5HQWi_HJrmVUug78slky8NFQA8NxGyoQIVMsNUzUALsTUJfZAHI6rBpxPQLUejRDnI1ZFbAJwtYq_-f7tFE_dpFheFywA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> The information in this e-mail is intended only for the person to whom it is >> addressed. 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