Dear Freesurfer team I am sorry to bore you again with my problems, but I need your help (or opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my Freesurfer version (5.0)? Or do I need to use the 5.3 version? I would prefer to avoid to install the 5.3 version, because I think that I would need to re-perform all the analyses from the beginning (that in my computer would be about two months at full-time working). If there is any other solution (or if I simply need to wait that you look for the best solution), please let me know. Thank you! Angela > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
