Copy this file into $FREESURFER_HOME/bin (make a backup of the existing one) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
let me know if that works doug
On 07/29/2014 05:37 PM, angela.favaro@unipd.it wrote:
I am using 5.3
make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: Flag --lh unrecognized. --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: make_average_surface
Is that all it prints out? What version of FS are you using?
On 07/29/2014 05:26 PM, angela.favaro@unipd.it wrote:
ERROR: Flag --lh unrecognized.
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 >>> >>> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom >> it >> is >> addressed. If you believe this e-mail was sent to you in error and >> the >> e-mail >> contains patient information, please contact the Partners >> Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you >> in >> error >> but does not contain patient information, please contact the sender >> and >> properly >> dispose of the e-mail. >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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