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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Corinna Bauer corinnab83@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 <corinnab83@gmail.commailto:corinnab83@gmail.com> wrote: Great, thanks. The nu.mgz is attached.

Corinna

On Wed, May 5, 2021 at 6:47 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 <BFISCHL@mgh.harvard.edumailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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). I attached a screenshot of orig.mgz viewed in fsleyes. Any thoughts?

Thanks!

Corinna

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1QClCCeXykBScK8d5iq23hqFkPyT2qn3mpaj7VqrhnWoppw9oWwy0qLPuD9BIPjTdeJa94TGnemkL_KiFjBw1Wab0D0mWH3IJcLKpIvh3BUof3t8xND1Fyb0C0Oy81H4-qCdUJdmt38iWTc8TpxDh5_Yw1cXNpgUms9JohWuBwdgsS9W1WTq8_GErqY8walozgYWnbL4e4RZVfRBjejiWh9MVvmJuNyYihX24Ofy5tor4iJ4p6qic2UQYV5acvEbhCfxcST0sNEFjuaaYSdzHLQ/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. 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1rULMMfo2yJZfoOtKTGPpqqVNGJEBAprhcfVvdoBUoB2M0U0LN5Ib1EmDrEwQfMWyMihkXLjDkVDLndLYfy5LwXkc2vTFFfgEsqlxu1Up3X5u6qkNt1teQQ3ueOG6_nKKWudRc97_roeP5hWFLwK0sDUKUgARPFXIL6ebknC7hNQA7vWbISK-LumLErCyu5lA70JfJWkS6yWDb1-Bdmr-4tEp00GK5pxZEw6q1D0rF_KaCCuOjrZWKvhLFOTDfUTDj_fwFuJkjnTG8VGbxhSYUw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1dzAvSjb2xg057o7RyKJZrQAEUSNDKYyNvvSNj-Q1W3fj-H7rQN0_ff1fiWYt1iDlHtBScp2B2qG_7V6pAC3VnocY5eFs09ranBO0u_df2FpxmcLu365FC1Y15JadBeoa_2tWHOeKnTqTJHjpUfi4lN96S0NtVGAhYVBzbw4nNZWWu5-xDrN-dnnMOECv_nfLkTj-OQ0D12o_YyFO9czOpW-8tR_HfnXEFCu5snUTMUT62UkuGNVpVyeJsWzZsaOxlxdGZqy1QTaz8wvCA_yC6w/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. 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1QIBq5EkkrXvBYedkVZBu1QSZSDY095TOl1_qa7F6M9d384V_TiBzx8rtP2y1LY0qUU937Ep76OvJeSNG8W7gn90zPnconlxQz3REgfCZywQqlAgNwXjqNdAdZihdoDU9SNgTfFRqLSzO8tdbadQfW7KqJUz31LrH45xNuWPKESmVgd98gF47tyGMjvEeOC1vEsOoTg-ordFAzjIiS67kMRUD2Sd1QZdv-7XVlY8o5eMZYbxyL0CYM0a4RndPXCYmfxcQBQ1FbWBoGZVJmbFzDA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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.