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 > > > > ______________________________________________________________________ > Hotmail: Free, trusted and rich email service. Get it now. > _______________________________________________ > 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
