ftp ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 331 Please specify the password. 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. 200 Switching to Binary mode. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. local: make_average_surface remote: make_average_surface 229 Entering Extended Passive Mode (|||37856|). 150 Opening BINARY mode data connection for make_average_surface (19641 bytes). 100% |***********************************| 19641 95.79 KiB/s 00:00 ETA 226 Transfer complete. 19641 bytes received in 00:00 (54.68 KiB/s) 221 Goodbye. [host-002:~/Desktop/risonanze/studyfree] angelafavaro% cp make_average_surface $FREESURFER_HOME/bin/make_average_surface cp: /Applications/freesurfer/bin/make_average_surface: Permission denied [host-002:~/Desktop/risonanze/studyfree] angelafavaro% sudo cp make_average_surface $FREESURFER_HOME/bin/make_average_surface Password: [host-002:~/Desktop/risonanze/studyfree] angelafavaro% 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 23:57:25 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 23:57:27 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 > can you send the full terminal output > On 07/29/2014 06:00 PM, angela.fav...@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.fav...@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.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 >>>> >>>> >>> -- >>> 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
