Hi Corinna, I’m following up on your question to help you get this get resolved. I don’t see the data that has been attached. Can you try resending your input data for mri_nromalize and I will try to run this?
Best, Ren From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Corinna Bauer <corinna...@gmail.com> Date: Thursday, June 3, 2021 at 7:28 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage with MP2RAGE data External Email - Use Caution Hi Bruce, I am just following up on this. Were you able to get mri_normalize to run on this mp2rage data? Thanks, Corinna On Wed, May 5, 2021 at 6:50 PM Corinna Bauer <corinna...@gmail.com<mailto:corinna...@gmail.com>> wrote: Great, thanks. The nu.mgz is attached. Corinna On Wed, May 5, 2021 at 6:47 PM Fischl, Bruce <bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote: Hmmmm, if you send us the data we will take a look. Just the inputs to mri_normalize should do it for this case Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Corinna Bauer Sent: Wednesday, May 5, 2021 6:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage with MP2RAGE data External Email - Use Caution Hi Bruce, The nu.mgz input into mri_normalize looks ok to me (screenshot attached), as does the talairach registration. Corinna On Wed, May 5, 2021 at 5:39 PM Fischl, Bruce <bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote: Can you take a look at the volume that was the input to mri_normalize and see if it looks ok? And check the talairach From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Corinna Bauer Sent: Wednesday, May 5, 2021 5:25 PM To: Mailing Freesurfer List <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] error at 3d normalization pass 1 of 2 stage with MP2RAGE data External Email - Use Caution Hello all, I am trying to run recon-all on MP2RAGE data from Philips and it exits with errors at this point: 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 The log file is attached. The input file was the MPRAGE generated on the scanner console (i.e. not the T1 map). 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