I have been able to replicate the error with the patch in 5.1 and I'm working on a fix. doug
On 07/07/2014 10:52 AM, angela.fav...@unipd.it wrote: > 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 > > -- 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
