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, [email protected] 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, [email protected] 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 >>>>> [email protected] >>>>> 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 >>>> [email protected] >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> [email protected] >>> 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 >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
_______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
