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.fav...@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.fav...@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.fav...@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 >>>>> gr...@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 >>> gr...@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 > gr...@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
