Try adding --lh to the make_average_subject command line. Let me know if that works and I'll change the docs doug
On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote:
Hi Doug, this the command and output (here with only five subjects). thank you!
make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only
/Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only
$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Mar 29 Lug 2014 23:09:30 CEST /Users/angelafavaro/Desktop/risonanze/studyfree setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree uid=501(angelafavaro) gid=20(staff) groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) ==================== make_average_surface ==================== Mar 29 Lug 2014 23:09:31 CEST /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only input subjects: subj001 subj002 subj003 subj004 subj005 output subject: myatlas.i1 mri_add_xform_to_header -c auto /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz INFO: extension is mgz
#@# Making lh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...
processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... curvature mean = -0.028, std = 0.969 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm...
processing subject subj001/xhemi (2 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.586 curvature mean = -0.082, std = 0.795 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... curvature mean = -0.026, std = 1.007 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm...
processing subject subj002 (3 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.593 curvature mean = -0.071, std = 1.122 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... curvature mean = -0.025, std = 0.999 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm...
processing subject subj002/xhemi (4 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.597 curvature mean = -0.059, std = 1.231 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... curvature mean = -0.032, std = 0.973 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm...
processing subject subj003 (5 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.603 curvature mean = -0.062, std = 0.880 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... curvature mean = -0.035, std = 0.995 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm...
processing subject subj003/xhemi (6 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.572 curvature mean = -0.070, std = 2.235 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... curvature mean = -0.039, std = 0.991 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm...
processing subject subj004 (7 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.586 curvature mean = -0.097, std = 4.940 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... curvature mean = -0.028, std = 1.002 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm...
processing subject subj004/xhemi (8 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.603 curvature mean = -0.069, std = 1.134 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... curvature mean = -0.025, std = 1.004 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm...
processing subject subj005 (9 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.622 curvature mean = -0.067, std = 0.915 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... curvature mean = -0.038, std = 0.967 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm...
processing subject subj005/xhemi (10 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.591 curvature mean = -0.078, std = 0.997 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... curvature mean = -0.030, std = 0.984 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... writing updated template with 10 subjects to lh.reg.template.tif... curvature mean = 0.003, std = 0.598 curvature mean = -0.080, std = 0.911
#@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...
processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface [host-002:~/Desktop/
What is the command line that is failing and what is the full terminal output? doug
On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote:
Hi all, I am now working with the 5.3 version and performing interhemispheric registration (building my own atlas)
after running for all subjects: xhemireg --s subj001.... surfreg --s subj001 --t fsaverage_sym --lh surfreg --s subj001 --t fsaverage_sym --xhemi --lh
I have tried first iteration, but the following error occurs:
processing subject subj001 (1 of 194) reading spherical surface /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface
how can I get the rh.fsaverage_sym.sphere.reg file?
thank you!
Angela
Hi Matt
certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look? cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:
Hello Freesurfer team, I've used freesurfer to segment (recon-all) approximately 30 different subjects from a study. I've noticed that a large number of these subjects have a misclassification of the white and pial boundaries in the occipital lobe (such that grey matter is being classified as white matter). I believe this problem is originating from my scanner and original data. I'm acquiring a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel phased array head coil. For many subjects, this acquistion gives intensity inhomogeneity in the occipital lobe. I've begun using a GE based correction technique (PURE) on the images, and it appears to improve the intensity in the occipital lobe, but Freesurfer is still frequently misclassifying.
I'm wondering what would be the best way to edit the data. I've often tried to edit the wm.vol, but this doesn't seem to fix anything. For the most part, the wm.vol is correct to begin with, but the wm cutting line isn't segmenting with the wm.vol. I've also tried to add control points but this doesn't seem to improve anything either.
I've attached an image which I hope will further explain my problems.
Thanks for any help
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