Hi Doug, a further question: my final symmetric atlas seems to be not inflated enough, but still have important sulcations. Do I have to perform further iterations (myatlas.i4, myatlas.i5 ....) until the resulting volume is good enough? Or which is the correct method (other than performing asymmetry analyses on fsaverage_sym, that I will do) in this case?
thank you! Angela > sorry, I should have given you a new make_average_volume. > > you can get it from here > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_volume > > > On 08/11/2014 07:52 AM, angela.fav...@unipd.it wrote: >> Hi Doug, I am having a problem with the last step of building my own >> symmetric atlas. I am using the make_average_surface you gave me and >> adding the --lh flag in the first two iteration. >> However in the third iteration the command 'make_average_subject' did >> not >> recognize neither the --hemi lh flag (indicated in the wiki guide) >> neither >> the --lh flag (you suggested to add in the first two iterations) >> >> the error message was immediate in the first case: >> ERROR: Flag --hemi unrecognized. >> >> and after two hours in the second... >> ERROR: Flag --lh unrecognized. >> --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --subjects subj001 >> subj002 .... --xhemi --lh >> ERROR: make_average_volume >> >> Do you think I need a 'special' make_average_volume? or I need to use >> the >> 'old' 'make_average_surface'? >> >> the log of make_average_surface in the script folder of my atlas.i3 >> indicates no error... (attached) >> >> thank you for any help!! >> >> Angela >> >> >> >> >> >>> when you run make_average_subject, you will still need the --lh >>> doug >>> >>> On 07/29/2014 06:07 PM, angela.fav...@unipd.it wrote: >>>> 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 >>>> >>>> >>> -- >>> 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
