External Email - Use Caution
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
It is not clear what is failing. Can you check two things? 1. Check the talairach.lta with cd $SUBJECTS_DIR/subject/mri/transforms tkregisterfv --mov ../orig.mgz --reg talairach.lta --targ $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca This does not have to be perfect, but it should not be way off (ie, more than 10mm or 20 deg) 2. Look at the brainmask.mgz to see whether too much or too little of the skull was removed
If those things look ok, then upload the subject so I can take a look using the steps below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 5/16/2020 3:32 PM, Schranzer René wrote:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Schranzer René