Dear Freesurfer experts,

 

I'm trying to recon-all (-hires) for a new subject (mp2rage image) using the FreeSurfer Version 7.1. However, the recon-all exited with errors at the "mri_ca_normalize". I also processed the same subject from different timepoints and they finished without errors.

 

The error log is as following:

 

#@# CA Normalize Sat May 16 12:43:31 CEST 2020

/data/disk_1/IP/MS/freesurfer/MS_MRS_03_TP1_MP2RAGE/mri

 

mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz

 

writing control point volume to ctrl_pts.mgz

using MR volume brainmask.mgz to mask input volume...

reading 1 input volume

reading atlas from '/usr/local/freesurfer/average/RB_all_2020-01-02.gca'...

reading transform from 'transforms/talairach.lta'...

reading input volume from nu.mgz...

MRImask(): AllowDiffGeom = 1

resetting wm mean[0]: 98 --> 107

resetting gm mean[0]: 61 --> 61

input volume #1 is the most T1-like

using real data threshold=6.0

skull bounding box = (74, 87, 47) --> (250, 243, 247)

finding center of left hemi white matter

using (133, 139, 147) as brain centroid of Right_Cerebral_White_Matter...

MRImask(): AllowDiffGeom = 1

mean wm in atlas = 107, using box (111,120,122) --> (154, 158,171) to find MRI wm

before smoothing, mri peak at 109

robust fit to distribution - 108 +- 4.3

after smoothing, mri peak at 109, scaling input intensities by 0.982

scaling channel 0 by 0.981651

using 246437 sample points...

INFO: compute sample coordinates transform

0.82947  -0.03916   0.01418  -3.56121;

0.02560   0.95026   0.20358  -65.47982;

-0.02149  -0.16312   0.83311   18.21485;

0.00000   0.00000   0.00000   1.00000;

INFO: transform used

finding control points in Left_Cerebral_White_Matter....

found 40230 control points for structure...

bounding box (162, 90, 50) --> (242, 211, 245)

double free or corruption (out)

Command terminated by signal 6

@#@FSTIME  2020:05:16:12:43:32 mri_ca_normalize N 8 e 52.08 S 0.30 U 41.78 P 80% M 793644 F 0 R 213860 W 0 c 1239 w 3 I 0 O 0 L 10.49 12.64 12.79

@#@FSLOADPOST 2020:05:16:12:44:24 mri_ca_normalize N 8 10.29 12.25 12.65

Linux twodogs 4.15.0-88-generic #88-Ubuntu SMP Tue Feb 11 20:11:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s MS_MRS_03_TP1_MP2RAGE exited with ERRORS at Sat May 16 12:44:24 CEST 2020

 

 

I am thankful for any help.

 

Best,

René