Hi, there,
I am running rebuild_gca_atlas.csh now, and met a problem at the first
mri_ca_normalize step, my rebuild_gca_atlas.log file looks like below,
....................
\n\n
mri_ca_normalize -mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/brain.mgz
-seg
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/seg_edited.mgz
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/nu.mgz
noatlas noxform
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/norm.mgz
mri_ca_normalize -mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/brain.mgz
-seg
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/seg_edited.mgz
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/nu.mgz
noatlas noxform
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/norm.mgz
mri_ca_normalize -mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/brain.mgz
-seg
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/seg_edited.mgz
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/nu.mgz
noatlas noxform
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/norm.mgz
mri_ca_normalize -mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/brain.mgz
-seg
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/seg_edited.mgz
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/nu.mgz
noatlas noxform
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/norm.mgz
\n\n
......................
Is this noatlas noxform valid here, should it be -noatlas -noxform?
Actually, what I got from my terminal is;
Log file is
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/rebuild_gca_atlas_2010-02-01.log
mri_ca_normalize each subject using its seg_edited.mgz, producing norm.mgz...
mri_ca_normalize -mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/brain.mgz
-seg
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/seg_edited.mgz
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/nu.mgz
noatlas noxform
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/norm.mgz
Unable to read script file because of error: error opening mri_ca_normalize
-mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/bra:
No such file or directory
mri_ca_normalize -mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/brain.mgz
-seg
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/seg_edited.mgz
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/nu.mgz
noatlas noxform
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/norm.mgz
Unable to read script file because of error: error opening mri_ca_normalize
-mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502:
No such file or directory
mri_ca_normalize -mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/brain.mgz
-seg
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/seg_edited.mgz
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/nu.mgz
noatlas noxform
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/norm.mgz
Unable to read script file because of error: error opening mri_ca_normalize
-mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523:
No such file or directory
mri_ca_normalize -mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/brain.mgz
-seg
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/seg_edited.mgz
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/nu.mgz
noatlas noxform
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/norm.mgz
Unable to read script file because of error: error opening mri_ca_normalize
-mask
/home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129:
No such file or directory
But all the files and directories are there? any suggestions?
Thanks!
Guang
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