Can you send the recon-all.log file?

On 1/31/2022 5:02 AM, Dr. Cornelius Kronlage wrote:

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Dear Falk,

thanks for the hint! My understanding was that the "robust" MP2 actually reintroduces some of the field inhomogeneity artefacts that MP2RAGE is designed to compensate (OBrien Plos One 2014) - that's why I am trying to go with skullstripping... That way, the majority of > 100 volumes here is processed just fine, too. Don't know what is causing the problem in some.

Best wishes Cornelius

-----Ursprüngliche Nachricht----- Von: falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de Gesendet: Montag, 31. Januar 2022 10:45 An: 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu Cc: Dr. Cornelius Kronlage Cornelius.Kronlage@med.uni-tuebingen.de Betreff: AW: mri_normalize error MP2RAGE

Hi Cornelius,

this doesn't address your issue directly and I may have simply been lucky, however, I haven't had any difficulties to process (7T) MP2RAGE data after background removal suggested by Marques et al. (https://secure-web.cisco.com/1j8Dv_p6-ZO7_HRDNVu0NxLOugspVR5H7LS6K731DKHjw2J... I'd omit the skullstripping, too.

Maybe this helps.

Best,

Falk

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Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Dr. Cornelius Kronlage Cornelius.Kronlage@med.uni-tuebingen.de Gesendet: Montag, 31. Januar 2022 10:14:22 An: 'freesurfer@nmr.mgh.harvard.edu' Betreff: [Freesurfer] mri_normalize error MP2RAGE

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Dear freesurfer experts,

when running recon-all (FS version 7.2.0) on skullstripped 3T MP2RAGE sequences, about 10-20% of scans from one scanner fail because of this:

     mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz

      [...]

     Iterating 2 times
     ---------------------------------
     3d normalization pass 1 of 2
     error: No such file or directory
     error: MRInormFindControlPoints: could not find enough control points
     error: No such file or directory
     error: MRInormFindControlPoints failed
     Command exited with non-zero status 253

nu.mgz as the input to mri_normalize looks good to me. I am of course happy to provide full logs and some example data - please let me know.

The exact same problem (also MP2RAGE data) has been described twice before, but I couldn't find a solution: https://secure-web.cisco.com/1r3_UfItk0odyQTEjL22mLAxycj89_vXfN--AkpFwUzred-... https://secure-web.cisco.com/1_dIFX4W-YMl78kLd-J9E7AGEkpzUy7zCtCTsFt-L6nLdAv...

Thanks you in advance and best wishes

Cornelius

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