Following a bug-fix to enable processing large number of scans in make_average_surface
( see  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14122.html )
Something odd has happpened and I am not able to run the make_average as before.
I am trying to make an average map of a single subject using
make_average_subject --out aMPRAGE01 --subjects MPRAGE01

But after few minutes I get the following error message
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
make_average_surface --out aMPRAGE04 --subjects MPRAGE04
$Id: make_average_surface,v 1.39.2.2 2009/07/30 23:33:52 nicks Exp $
Mon Aug  9 16:32:52 BST 2010
/Applications/freesurfer/subjects/areamap
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/areamap ni305.cor.mgz
INFO: extension is mgz

output ddir is /Applications/freesurfer/subjects/areamap
uid=501(Lena) gid=20(staff) groups=20(staff),98(_lpadmin),81(_appserveradm),101(com.apple.sharepoint.group.1),79(_appserverusr),80(admin),102(com.apple.access_ssh)
====================
make_average_surface
====================
Mon Aug  9 16:32:52 BST 2010
/Applications/freesurfer/subjects/areamap
/Applications/freesurfer/bin/make_average_surface
--out aMPRAGE04 --subjects MPRAGE04
input subjects: MPRAGE04
output subject: aMPRAGE04
mri_add_xform_to_header -c auto /Applications/freesurfer/subjects/areamap/aMPRAGE04/mri/mni305.cor.mgz /Applications/freesurfer/subjects/areamap/aMPRAGE04/mri/mni305.cor.mgz
#@# Making lh registration template ---------
/Applications/freesurfer/subjects/areamap/aMPRAGE04
mris_make_template -norot -annot aparc lh sphere.reg MPRAGE04 lh.reg.template.tif
not aligning hemispheres before averaging.
zeroing medial wall in aparc
creating new parameterization...

processing subject MPRAGE04 (1 of 1)
reading spherical surface /Applications/freesurfer/subjects/areamap/MPRAGE04/surf/lh.sphere.reg...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)
ripping medial wall...
computing parameterization for surface /Applications/freesurfer/subjects/areama/MPRAGE04/surf/lh.inflated.H...
curvature mean = -0.027, std = 1.004
computing parameterization for surface /Applications/freesurfer/subjects/areamap/MPRAGE04/surf/lh.sulc...
computing parameterization for surface /Applications/freesurfer/subjects/areamap/MPRAGE04/surf/lh.smoothwm...
writing updated template with 1 subjects to lh.reg.template.tif...
curvature mean = -0.004, std = 0.594
curvature mean = -0.066, std = 0.792
#@# Making lh annotation ---------------------
Mon Aug  9 16:33:07 BST 2010
mris_ca_label -ml-annot lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs 7 label/lh.aparc.annot
/Applications/freesurfer/subjects/areamap/aMPRAGE04
ML Label: lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs 7 label/lh.aparc.annot
   Reading icosahedron /Applications/freesurfer/lib/bem/ic7.tri
Reading gcsa from /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs
reading color table from GCSA file....
average std = 2.1   using min determinant for regularization = 0.044
0 singular and 372 ill-conditioned covariance matrices regularized
Building most likely labels
Filtering labels
2 filter iterations complete (2 requested, 378 changed)
writing colortable into annotation file...
mris_ca_label -ml-annot lh.destrieux.simple.2009-07-29.gcs 7 label/lh.aparc.a2009s.annot
/Applications/freesurfer/subjects/areamap/aMPRAGE04
ML Label: lh.destrieux.simple.2009-07-29.gcs 7 label/lh.aparc.a2009s.annot
   Reading icosahedron /Applications/freesurfer/lib/bem/ic7.tri
Reading gcsa from /Applications/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs
reading color table from GCSA file....
average std = 3.9 0.2   using min determinant for regularization = 0.000
0 singular and 1066 ill-conditioned covariance matrices regularized
Building most likely labels
Filtering labels
2 filter iterations complete (2 requested, 1605 changed)
writing colortable into annotation file...
#@# Making average lh.orig surface ---------------------
Mon Aug  9 16:33:21 BST 2010
/Applications/freesurfer/subjects/areamap/aMPRAGE04
mris_make_average_surface -i 7 -o orig -sdir-out /Applications/freesurfer/subjects/areamap lh orig_avg sphere.reg aMPRAGE04 MPRAGE04
/Applications/freesurfer/bin/mris_make_average_surface: Permission denied.
mris_average_surface failed
ERROR: make_average_surface


+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


Any help will be much appreciated,

Thanks
Lena

_______________________________________________________
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH

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