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Hello FreeSurfer developers,
I am attempting to run the mri_normalize function on T1 MPRAGE data and some of my subjects get an error: 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
This error comes up with some subjects but not others in the group with the same acquisition details. It is cross vendor (it has come up for both Siemens and Philips).
Strangely enough, when I gave the data to someone else to run on their end, mri_normalize worked just fine... they are running FreeSurfer 5.3.0.
On my own computer, running freesurfer version 7, I can get it to work by changing the orientation using mri_convert... though most subjects work with the original input orientation, and I would prefer not to have to do what feels like an arbitrary orientation change.
Do you know why this could be happening? Were there any changes made to the mri_normalize function between v5.3.0 and v7?
Thank you so much for any advice.
Zoe O'Brien-Moran
First, can you send the full command line and terminal output? Second, what are you trying to do? Are you running this outside of recon-all? If so, why?
On 5/11/2022 5:55 PM, Zoe O'Brien-Moran wrote:
External Email - Use Caution
Hello FreeSurfer developers,
I am attempting to run the mri_normalize function on T1 MPRAGE data and some of my subjects get an error: *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*
This error comes up with some subjects but not others in the group with the same acquisition details. It is cross vendor (it has come up for both Siemens and Philips).
Strangely enough, when I gave the data to someone else to run on their end, mri_normalize worked just fine... they are running FreeSurfer 5.3.0.
On my own computer, running freesurfer version 7, I can get it to work by changing the orientation using mri_convert... though most subjects work with the original input orientation, and I would prefer not to have to do what feels like an arbitrary orientation change.
Do you know why this could be happening? Were there any changes made to the mri_normalize function between v5.3.0 and v7?
Thank you so much for any advice.
Zoe O'Brien-Moran
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you for the response, I am so sorry for the late reply -- response went to junk, so I just saw it.
To confirm my theory that it was a version issue, I downloaded V5.3.0 as well and confirmed that the scan is normalized using V5.3.0 but "fails" using the exact same input using V7.
The output is attached.
I am using it outside of recon-all because it is used as a step in an algorithm for converting MPRAGE MR data to a "pseudo"CT image.
I cannot speak to the specifics of why it was used in this case, because I didn't write the algorithm or scripts (received is a package).
That aside, it is strange that the mri_normalize function fails on the same data set was V7.2.0 but works with version 5.3.0. Now that I can toggle between versions, it is clear it is just an issue with the version. Is it possible there are different defaults with V7.2.0?
Thanks in advance, and sorry again for the delayed response to your reply ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Thursday, May 12, 2022 2:59 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_normalize issues, Version 7
First, can you send the full command line and terminal output? Second, what are you trying to do? Are you running this outside of recon-all? If so, why?
On 5/11/2022 5:55 PM, Zoe O'Brien-Moran wrote:
External Email - Use Caution
Hello FreeSurfer developers,
I am attempting to run the mri_normalize function on T1 MPRAGE data and some of my subjects get an error: 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
This error comes up with some subjects but not others in the group with the same acquisition details. It is cross vendor (it has come up for both Siemens and Philips).
Strangely enough, when I gave the data to someone else to run on their end, mri_normalize worked just fine... they are running FreeSurfer 5.3.0.
On my own computer, running freesurfer version 7, I can get it to work by changing the orientation using mri_convert... though most subjects work with the original input orientation, and I would prefer not to have to do what feels like an arbitrary orientation change.
Do you know why this could be happening? Were there any changes made to the mri_normalize function between v5.3.0 and v7?
Thank you so much for any advice.
Zoe O'Brien-Moran
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1_IJ8QCGknt-zzTGTt0yCg9FalibeQVztjVpTEGPaA_aWeK...
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Yes, there might be a lot of changes between 7.2 and 5.3
On 5/26/2022 1:12 PM, Zoe O'Brien-Moran wrote:
External Email - Use Caution
Thank you for the response, I am so sorry for the late reply -- response went to junk, so I just saw it.
To confirm my theory that it was a version issue, I downloaded V5.3.0 as well and confirmed that the scan is normalized using V5.3.0 but "fails" using the exact same input using V7.
The output is attached.
I am using it outside of recon-all because it is used as a step in an algorithm for converting MPRAGE MR data to a "pseudo"CT image.
I cannot speak to the specifics of why it was used in this case, because I didn't write the algorithm or scripts (received is a package).
That aside, it is strange that the mri_normalize function fails on the same data set was V7.2.0 but works with version 5.3.0. Now that I can toggle between versions, it is clear it is just an issue with the version. Is it possible there are different defaults with V7.2.0?
Thanks in advance, and sorry again for the delayed response to your reply
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU *Sent:* Thursday, May 12, 2022 2:59 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_normalize issues, Version 7 First, can you send the full command line and terminal output? Second, what are you trying to do? Are you running this outside of recon-all? If so, why?
On 5/11/2022 5:55 PM, Zoe O'Brien-Moran wrote:
External Email - Use Caution
Hello FreeSurfer developers,
I am attempting to run the mri_normalize function on T1 MPRAGE data and some of my subjects get an error: *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*
This error comes up with some subjects but not others in the group with the same acquisition details. It is cross vendor (it has come up for both Siemens and Philips).
Strangely enough, when I gave the data to someone else to run on their end, mri_normalize worked just fine... they are running FreeSurfer 5.3.0.
On my own computer, running freesurfer version 7, I can get it to work by changing the orientation using mri_convert... though most subjects work with the original input orientation, and I would prefer not to have to do what feels like an arbitrary orientation change.
Do you know why this could be happening? Were there any changes made to the mri_normalize function between v5.3.0 and v7?
Thank you so much for any advice.
Zoe O'Brien-Moran
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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/freesurfer https://secure-web.cisco.com/1_IJ8QCGknt-zzTGTt0yCg9FalibeQVztjVpTEGPaA_aWeKlqcQ9Exs8brPj2ljsXP1iGI6GN2wNhp5bLPnEWrK-OIyy60MvE8TuMkVm-bHealBlC1hfXXe_zrIMElkrzWgZuSc2XJkB-GQYQcObP23IURGes6c0nQOJzxGBJQA_qR_dFIj1EgkvAiVt2HeNVzk2m9wG5rVkPY4YGVMYqDQLmdrPOf3k4eD6zSPeuoOSAo9n4rPl8nzF9HL46nkGBeVqCFmFyz7L0GlZzK4xKeDbvEJ-2L2fWCsYnDbByZ_k8gjJE6BxPXIFbq2n7zVfv3k6stCLR4uT732b8f7pr8A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Douglas N. Greve -
Zoe O'Brien-Moran