ok thanks a lot for the quick answer. let me know when it works. our mri voxel size is 1 mm isotropic. (if it changes anything, I am working on ubuntu 14.04).
Cheers, Pierre On Wed, Jul 20, 2016 at 11:15 AM, Iglesias, Eugenio <e.igles...@ucl.ac.uk> wrote: > Thanks a lot, Pierre. > I’ll get this sorted out as soon as possible. I’m in the process of > modifying the module so it supports data with resolution >1mm, and also > incorporating the longitudinal segmentation method described in > https://doi.org/10.1016/j.neuroimage.2016.07.020 > Cheers, > Eugenio > > Juan Eugenio Iglesias > Translational Imaging Group > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > On 20 Jul 2016, at 09:57, pierre deman <deman.pie...@gmail.com> wrote: > > Hi, > > I downloaded the new freesurfer development version and I still have the > same problem when running the hippocampal-subfields > > "Invalid MEX-file > '/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64': > libkvlGEMSCommon.so: cannot open shared object file: No such file or > directory > Error in kvlClear (line 11) > > Error in segmentSubjectT1_autoEstimateAlveusML (line 133) > > MATLAB:invalidMEXFile". > > Does anyone have any idea about a solution ? > > Cheers, > Pierre > > > On Wed, Jul 13, 2016 at 12:22 PM, Iglesias, Eugenio <e.igles...@ucl.ac.uk> > wrote: > >> And thanks to Zeke, of course ;-) >> >> >> Juan Eugenio Iglesias >> Translational Imaging Group >> University College London >> http://www.jeiglesias.com >> http://cmictig.cs.ucl.ac.uk/ >> >> >> On 13 Jul 2016, at 11:19, Iglesias, Eugenio <e.igles...@ucl.ac.uk> wrote: >> >> Dear all, >> our expert developer Zeke Kaufman figured out what the problem was. We >> have now fixed the Linux version; the MAC version will hopefully be ready >> as well in a couple of days. I have also fixed other bugs (including the >> problem that caused the code to get stuck every once in a while). >> You can downloaded the latest development version from our website. >> Thanks everyone for your feedback. >> Cheers, >> Eugenio >> >> >> >> Juan Eugenio Iglesias >> Translational Imaging Group >> University College London >> http://www.jeiglesias.com >> http://cmictig.cs.ucl.ac.uk/ >> >> >> On 8 Jul 2016, at 12:14, Iglesias, Eugenio <e.igles...@ucl.ac.uk> wrote: >> >> I think I identified the problem; hopefully this will be sorted out very >> soon. >> Cheers, >> Eugenio >> >> Juan Eugenio Iglesias >> Translational Imaging Group >> University College London >> http://www.jeiglesias.com >> http://cmictig.cs.ucl.ac.uk/ >> >> >> On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis < >> rpereacama...@mgh.harvard.edu> wrote: >> >> *Warning: This message has had one or more attachments removed >> (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s) >> for more information.* >> Hi all, >> I am currently trying to run hippocampal subfields in a couple of my >> participants using FreeSurfer6.0 (located at >> *nmr*:/usr/local/freesurfer/stable6). >> >> It did run successfully for many of my subjects earlier in the year but >> some of them only had a let hemisphere segmentation. So I decided to re-run >> them using launchpad and also my local nmr computer. >> >> Now, none of the hippocampal sufields segmentations appear (no >> rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at >> <FSSUBJECT>/scripts/scripts/hippocampal-subfields-T1T2.log and the error I >> get is: >> >> Error:Cannot find CTF archive >> /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf >> >> >> Could a missing *.ctf cause the error? (btw, the re-run happened after >> the major hardware crash). >> >> Thanks in advance for your help, >> Rodrigo >> >> PS: I am attaching the *log files as suggested in the bug reporting page. >> >> >> --- >> Rodrigo Dennis Perea >> Research Fellow >> Department of Radiology >> Athinoula A. Martinos Center >> Massachusetts General Hospital >> rpereacama...@mgh.harvard.edu >> >> >> >> >> >> >> This is a message from the E-Mail Virus Protection System at UCL >> ---------------------------------------------------------------------- >> >> The original e-mail attachment (recon-all.cmd) is on the list of >> unacceptable attachments for UCL and has been replaced by this >> warning message. This constraint is in place to protect users >> from viruses and other malware. >> >> If you think this attachment is a legitimate file and you wish to >> receive it, please ask the sender to rename the file extension (eg >> rename file.exe to file.ex_) and resend it to avoid this constraint. >> On receiving the file you will have to save it and rename it back to >> its original extension. >> >> >> Reference: 1bLDxs-0003ZW-3F >> >> -- >> UCL E-mail Virus Protection System >> serviced...@ucl.ac.uk >> Internal phone: 25000 >> >> >> <hippocampal-subfields-T1T2.log><recon-all.log> >> _______________________________________________ >> 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 >> >> >> 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. >> >> > > > -- > DEMAN Pierre > Mobile : +33 7 82 57 80 94 > _______________________________________________ > 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. > > -- DEMAN Pierre Mobile : +33 7 82 57 80 94
_______________________________________________ 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.
