[Freesurfer] recon-all exited with errors

hi all, I ran recon-all on a case, and it exited with errors, and the error message looks like this: ERROR: Talairach QA check failed! z-score = -6 = -6 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check

[Freesurfer] recon-all

Hi guys, I have the raw PAR REC and DICOM files from the scanner. I converted the PAR REC files to mgz and ran recon-all but it exited with errors. But when I converted the DICOM files into mgz and ran recon-all, it was running fine. Can anyone tell me why this is happening. Regards, Sameer

Re: [Freesurfer] recon-all

Yes, I used the dicom to run recon-all. I converted the results back to native space, using mri_convert -rl orig/001.mgz XX.mgz XX_native.mgz the images in the native space are not in the same orientation as 001.mgz, which i got from the dicoms. ___

Re: [Freesurfer] recon-all

I am using mricro to view the images. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Re: Atlases

Hi all, I am trying to find the atlases in the freesurfer directory. I could not find the specific atlases sub directory. Is there a sub directory that contains all the atlases like the MNI, JHU, etc? Regards, Sameer Kumar Gottipati ___ Freesurfer

[Freesurfer] Re: Atlas

Hi all, I am trying to find the sub directory in the Freesurfer directory which contains all the atlases like MNI, JHU, etc. Can you please help me out... Thanks, Regards, Sameer Kumar Gottipati ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] mri_convert

Hi all, It says .mgz file not found. I am new to FS so please help me out with this. Thanks, Regards, Sameer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_convert

The output files of recon-all ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_convert

Hi all, I am new to FS and I would like to know the usage of mri_convert to convert the results of FreeSurfer into the analyze format. Thanks, Regards, Sameer Kumar Gottipati ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https