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). I attached a screenshot of orig.mgz
viewed in fsleyes. Any thoughts?
Thanks!
Corinna
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