OK, I have updated ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi
with new versions of mri_surf2surf and xhemireg. Copy those into $FREESURFER_HOME/bin (after making backups of what is already there) doug On 07/07/2014 03:24 PM, angela.fav...@unipd.it wrote: > Hi Doug, > thank you very much! > Angela > >> 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 >> >> > > > _______________________________________________ > 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
