can you send the full terminal output On 07/29/2014 06:00 PM, angela.favaro@unipd.it wrote:
Hi Doug, unfortunately the same error message appear... it looks for rh.fsaverage_sym.sphere.reg
.... #@# 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
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/
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-- 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/
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-- 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/
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