Hello FreeSurfer Developers,
I'm attempting to run the longitudinal stream, but in the [LONG] step of one time-point of on of my subjects, I have the following error:
MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 11 Starting OpenSpline(): npoints = 11 MRInormFindControlPoints: could not find enough control points building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 No such file or directory MRInormFindControlPoints failed No such file or directory
The segmentation of the this time-point for this subject ([CROSS] step) looks good and I couldn't find any error. I didn't find any similar error in the email list. Does anyone have any thoughts on how to trouble-shoot this one? I attached the recon-all.log.
FS version: freesurfer-linux-centos7_x86_64-dev-20181130-24625d8
Thanks, Gabriela
Does the orig.mgz file look ok?
On 11/30/2018 01:14 PM, Figueiro Longo, Maria Gabriela wrote:
Hello FreeSurfer Developers,
I'm attempting to run the longitudinal stream, but in the [LONG] step of one time-point of on of my subjects, I have the following error:
MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 11 Starting OpenSpline(): npoints = 11 MRInormFindControlPoints: could not find enough control points building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
Iterating 2 times
3d normalization pass 1 of 2 No such file or directory MRInormFindControlPoints failed No such file or directory
The segmentation of the this time-point for this subject ([CROSS] step) looks good and I couldn't find any error. I didn't find any similar error in the email list. Does anyone have any thoughts on how to trouble-shoot this one? I attached the recon-all.log.
FS version: freesurfer-linux-centos7_x86_64-dev-20181130-24625d8
Thanks, Gabriela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes.
The images have lower SNR but we ran other subjects with similar acquisition parameters and we didn't have problems.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Thursday, December 6, 2018 3:46:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream - LONG step
Does the orig.mgz file look ok?
On 11/30/2018 01:14 PM, Figueiro Longo, Maria Gabriela wrote:
Hello FreeSurfer Developers,
I'm attempting to run the longitudinal stream, but in the [LONG] step of one time-point of on of my subjects, I have the following error:
MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 11 Starting OpenSpline(): npoints = 11 MRInormFindControlPoints: could not find enough control points building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
Iterating 2 times
3d normalization pass 1 of 2 No such file or directory MRInormFindControlPoints failed No such file or directory
The segmentation of the this time-point for this subject ([CROSS] step) looks good and I couldn't find any error. I didn't find any similar error in the email list. Does anyone have any thoughts on how to trouble-shoot this one? I attached the recon-all.log.
FS version: freesurfer-linux-centos7_x86_64-dev-20181130-24625d8
Thanks, Gabriela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It says "Could not find file ..". I wonder which one it is looking for.
Did you try to completely delete this long subject dir and re-run from scratch? Do other time points with this base go through? If not, you could re- run the base also.
Also when you open orig of all time points (from the long dirs), are they nicely registered?
Best, Martin
On Thu, 2018-12-06 at 18:06 +0000, Figueiro Longo, Maria Gabriela wrote:
yes. The images have lower SNR but we ran other subjects with similar acquisition parameters and we didn't have problems. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr. mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.har vard.edu> Sent: Thursday, December 6, 2018 3:46:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream - LONG step Does the orig.mgz file look ok?
On 11/30/2018 01:14 PM, Figueiro Longo, Maria Gabriela wrote:
Hello FreeSurfer Developers,
I'm attempting to run the longitudinal stream, but in the [LONG]
step
of one time-point of on of my subjects, I have the following error:
MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 11 Starting OpenSpline(): npoints = 11 MRInormFindControlPoints: could not find enough control points building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
Iterating 2 times
3d normalization pass 1 of 2 No such file or directory MRInormFindControlPoints failed No such file or directory
The segmentation of the this time-point for this subject ([CROSS] step) looks good and I couldn't find any error. I didn't find any similar error in the email list. Does anyone
have
any thoughts on how to trouble-shoot this one? I attached the recon-all.log.
FS version: freesurfer-linux-centos7_x86_64-dev-20181130-24625d8
Thanks, Gabriela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu