those command args are correct (no dash on either). your error appears to be something pertaining to your run environment (so i'm not sure i can help with that).
n.
On Mon, 2010-02-01 at 12:34 -0600, Guang Zeng wrote:
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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