Sorry, I have no idea what is going wrong. Try using a full head in stead of skull stripped image
On 6/24/2024 8:08 AM, Chen Yang wrote: > External Email - Use Caution > > Dear Douglas, > > we had checked the template and compared it to the standard template > (MNI152_T1_1mm_brain.nii.gz). Our template looks normal on orientation and we > don't see anything unusual (please see screenshot). The only difference is > our head is smaller (probably because it's children data). > > Therefore, I have two questions: > 1. Do you think that the head size could be the reason for the reconstruction > failure? I don't think it should be, because the reconstruction of individual > data has been going very well. > 2. After creating our template, we also used the commands below to fill holes > and normalize. The data type of output file is float, but we find that the > standard template has a data type of short. Do you think the data type might > influence the reconstruction? In fact, we also tried to change the datatype > to 'short', but there were obvious problems with the output image. > > # Fill holes and normalize > fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul > ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats > ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range > ANTS_QS_template_MNIS.nii.gz -odt float > > Thank you so much! > > Best regards, > Chen > > > ----- Original Message ----- >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >> Sent: Monday, 3 June, 2024 18:42:14 >> Subject: Re: [Freesurfer] Recon-all for a common template >> 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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If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Mass General Brigham >> Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline >> <https://www.massgeneralbrigham.org/complianceline> . >> Please note that this e-mail is not secure (encrypted). If you do not wish >> to >> continue communication over unencrypted e-mail, please notify the sender of >> this message immediately. Continuing to send or respond to e-mail after >> receiving this message means you understand and accept this risk and wish to >> continue to communicate over unencrypted e-mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). 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