mris_ca_label - Freesurfer

30 Aug 2011


      Hi all,
I have run FS one step by one step.  When i goto mris_ca_label, i got something error. I dont know which path should i goto to run this command.
When i goto $SUBJECTS_DIR or $SUBJECTS_DIR/subj/,  i will get the following information
MRISreadVertexPosition(lh.spere.reg): could not open file /media/Seagate/3D_SPGR/subjects/01A/surf/lh.spere.reg
No such file or directory
mris_ca_label: could not read spherical coordinate system from lh.spere.reg for 01A
No such file or directory
When i goto $SUBJECTS_DIR/subj/surf, i will get the following information 
MRISread(subjects/01A/surf/lh.smoothwm): could not open file
No such file or directory
mris_ca_label: could not read surface file subjects/01A/surf/lh.smoothwm for 01A
No such file or directory
I can find both the files in the surf directory. The tree list of the $SUBJECTS_DIR/subj/ is
|-- bem
|-- label
|   |-- lh.cortex.label
|   `-- rh.cortex.label
|-- mri
|   |-- aseg.auto.mgz
|   |-- aseg.auto_noCCseg.label_intensities.txt
|   |-- aseg.auto_noCCseg.mgz
|   |-- aseg.mgz
|   |-- brain.finalsurfs.mgz
|   |-- brainmask.auto.mgz
|   |-- brainmask.mgz
|   |-- brain.mgz
|   |-- filled.mgz
|   |-- filled-pretess127.mgz
|   |-- filled-pretess255.mgz
|   |-- lh.dpial.ribbon.mgz
|   |-- lh.dwhite.ribbon.mgz
|   |-- lh.ribbon.mgz
|   |-- mri_nu_correct.mni.log
|   |-- norm.mgz
|   |-- nu.mgz
|   |-- nu_noneck.mgz
|   |-- orig
|   |   `-- 001.mgz
|   |-- orig.mgz
|   |-- rawavg.mgz
|   |-- rh.dpial.ribbon.mgz
|   |-- rh.dwhite.ribbon.mgz
|   |-- rh.ribbon.mgz
|   |-- ribbon.mgz
|   |-- segment.dat
|   |-- T1.mgz
|   |-- talairach.label_intensities.txt
|   |-- talairach.log
|   |-- talairach_with_skull_2.log
|   |-- talairach_with_skull.log
|   |-- transforms
|   |   |-- bak
|   |   |-- talairach.auto.xfm
|   |   |-- talairach_avi.log
|   |   |-- talairach.lta
|   |   |-- talairach.m3z
|   |   |-- talairach_with_skull_2.lta
|   |   |-- talairach_with_skull.lta
|   |   `-- talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
|   |-- wm.asegedit.mgz
|   |-- wm.mgz
|   `-- wm.seg.mgz
|-- scripts
|   |-- build-stamp.txt
|   |-- csurfdir
|   |-- ponscc.cut.log
|   |-- recon-all.cmd
|   |-- recon-all.done
|   |-- recon-all.env
|   |-- recon-all.local-copy
|   |-- recon-all.log
|   `-- recon-all-status.log
|-- src
|-- stats
|-- surf
|   |-- error.log
|   |-- lh.after
|   |-- lh.area
|   |-- lh.area.mid
|   |-- lh.area.pial
|   |-- lh.avg_curv
|   |-- lh.before
|   |-- lh.curv
|   |-- lh.curv.pial
|   |-- lh.defect_borders
|   |-- lh.defect_chull
|   |-- lh.defect_labels
|   |-- lh.inflated
|   |-- lh.inflated.H
|   |-- lh.inflated.K
|   |-- lh.inflated.nofix
|   |-- lh.jacobian_white
|   |-- lh.new_orig_uncorrected
|   |-- lh.new_qsphere_uncorrected
|   |-- lh.orig
|   |-- lh.orig.nofix
|   |-- lh.pial
|   |-- lh.qsphere.nofix
|   |-- lh.smoothwm
|   |-- lh.smoothwm.nofix
|   |-- lh.sphere
|   |-- lh.sphere.reg
|   |-- lh.sulc
|   |-- lh.thickness
|   |-- lh.volume
|   |-- lh.white
|   |-- rh.after
|   |-- rh.area
|   |-- rh.area.mid
|   |-- rh.area.pial
|   |-- rh.avg_curv
|   |-- rh.before
|   |-- rh.curv
|   |-- rh.curv.pial
|   |-- rh.defect_borders
|   |-- rh.defect_chull
|   |-- rh.defect_labels
|   |-- rh.inflated
|   |-- rh.inflated.H
|   |-- rh.inflated.K
|   |-- rh.inflated.nofix
|   |-- rh.jacobian_white
|   |-- rh.new_orig_uncorrected
|   |-- rh.new_qsphere_uncorrected
|   |-- rh.orig
|   |-- rh.orig.nofix
|   |-- rh.pial
|   |-- rh.qsphere.nofix
|   |-- rh.smoothwm
|   |-- rh.smoothwm.nofix
|   |-- rh.sphere
|   |-- rh.sphere.reg
|   |-- rh.sulc
|   |-- rh.thickness
|   |-- rh.volume
|   `-- rh.white
|-- tmp
|-- touch
`-- trash
Thanks,
Haitao
Haitao Ge, Ph.D.
Research Center for Sectional and Imaging Anatomy 
Shandong University School of Medicine
44#, West Wenhua Rd.
Jinan 250012, Shandong
P.R.China
Tel: +86-15965644699
Email: haitao.ge@homail.com