Hello Angela, Have you tried just running the specific commands to get the output file you need?
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Anthony On 7/7/14, 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 -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: ad...@fiu.edu Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu Join the Society for the Study of Human Development: http://www.sshdonline.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
