Hi Adam, thank you for your mail. I am quite demoralized because I cannot get out of my problem and I am not receiving support from the mailing list. Which is, according to you, the solution? Do I need to install 5.3 version and re-analyse all my subjects from the beginning? Or do you think that I can install the 5.3 xhemireg (and surfreg) only?
I would be very grateful to receive any help or opinion Angela > Just to provide some additional insight, > > I noticed that the xhemireg file was missing from > <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg> > the ftp on January 28th, 2014 and emailed the listserv: > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html > > Doug quickly emailed back after hosting it with "sorry, try now". > > I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, > and got an identical error as Angela. > Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The > label directory is empty). > > For curiosity, I used v5.3.0 and compared log files. > > Differences: > *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* > --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each > hemi --> copies only surfaces --> generate annots/cortex label from > -cortparc > > cp surf/lh.curv {subject}/xhemi/surf/rh.curv > cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc > cp surf/lh.area {subject}/xhemi/surf/rh.area > cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial > cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial > cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv > cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H > cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K > cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness > Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, > but > fails because rh.cortex.label does not exist in {subject}/label/ directory > > *xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> > mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and > annots/labels for each hemi > > cp surf/lh.curv {subject}/xhemi/surf/rh.curv > cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc > cp surf/lh.area {subject}/xhemi/surf/rh.area > cp surf/lh.volume {subject}/xhemi/surf/rh.volume > cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness > cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H > cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial > cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid > cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial > cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K > > > *cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp > label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp > label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* > (Not explicit, but the ?h.cortex.label appears at the same time; > presumably > just from the corresponding ?h.aparc.annot) > > Hope that was helpful! > Adam Martersteck > > > On 01/28/2014 11:26 AM, Adam Martersteck wrote: >> >> Hi Freesurfer team, >> >> I noticed that the xhemireg file is missing from: >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg >> > > > On Thu, Jul 3, 2014 at 3:44 PM, <angela.fav...@unipd.it> wrote: > >> Hi all, >> I am trying again to perform Surface-based Interhemispheric Registration >> in another computer (same version of FS 5.0) and by building my own >> atlas. >> However, there is an error while running xhemireg command (please find >> the >> log attached). >> >> I also noted that the command xhemireg took a lot of time to run (more >> than 30 min) while you wrote on the wiki that it would take a few >> minutes >> to finish. >> >> If anyone can give some hints it would be great >> >> thank you >> >> Angela >> >> > >> > >> > I'm not sure why this is failing. Are there other things in the xhemi >> > folder? What version of FS are you using? >> > doug >> > >> > On 07/01/2014 11:06 AM, angela.fav...@unipd.it wrote: >> >> sure! thank you >> >> >> >> >> >>> Can you send the log file (or the full terminal output)? >> >>> On 06/30/2014 03:11 PM, angela.fav...@unipd.it wrote: >> >>>> Hi all, >> >>>> I have a problem with 'Surface-based Interhemispheric Registration' >> >>>> >> >>>> I followed the instructions and all seem to work, but the command: >> >>>> 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' >> >>>> >> >>>> finish with the error below >> >>>> (indeed in the xhemi/label directory, there is no file) >> >>>> >> >>>> What can I do? >> >>>> Thank you for any help! >> >>>> Angela >> >>>> >> >>>> #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 >> >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts >> >>>> \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz >> >>>> -seed >> >>>> 1234 subj024/xhemi rh ../surf/rh.sphere.reg >> >>>> >> /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs >> >>>> ../label/rh.aparc.annot \n >> >>>> No such file or directory >> >>>> mris_ca_label: could not open label file ../label/rh.cortex.label >> >>>> No such file or directory >> >>>> >> >>>> No such file or directory >> >>>> Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel >> Version >> >>>> 10.8.0: Tue Jun 7 16:33:36 PDT 2011; >> >>>> root:xnu-1504.15.3~1/RELEASE_I386 >> >>>> i386 >> >>>> >> >>>> recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 >> 17:44:52 >> >>>> CEST >> >>>> 2014 >> >>>> >> >>>> >> >>>> >> >>>> _______________________________________________ >> >>>> 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 >> >>> >> >>> >> >>> 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 >> >> >> 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 > > > 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
