Why did you do an lr reversal if it looked good? And when you say it looks good, what do you mean. One thing to double check is that the orientation looks ok. Load it in freeview. Up at the top you will see little brain images in coronal, sagital, and axial. When you click on one of those, the brain in the main image should become coronal, sag, or axial. If this does not happen, then something is wrong.
On 5/29/2024 10:47 AM, Chen Yang wrote: > External Email - Use Caution > > Hi Douglas, > > thanks so much for you reply. Yes, I checked the template and it looks good. > The orientation was in LAS originally then I did the Left-Right Reversal by > using the command "mri_convert --in_orientation RIA". Before or after the > reversal, I got the same error message. Here I attached the template, could > you please have a look in case of any clue? Thank you so much! > > Best, > Chen > > > > ----- Original Message ----- >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >> Sent: Wednesday, 29 May, 2024 15:26:25 >> Subject: Re: [Freesurfer] Recon-all for a common template >> 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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