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.gro up.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_fin al.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_killi any.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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You need to make it executable with
chmod a+x /Applications/freesurfer/bin/mris_make_average_surface
Lena Palaniyappan wrote:
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
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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