Nick, Thanks for your kind help. I uploaded my orig.mgz i.e. 001.mgz using Martinos center file drop.
Thanks Venkat On Mon, Jun 23, 2014 at 11:42 PM, Nick Schmansky, MGH < ni...@nmr.mgh.harvard.edu> wrote: > Venkat, > > Can you send me your orig.mgz so that I can attempt to replicate? > > Nick > > > On Mon, 2014-06-23 at 08:46 +0530, Venkateswaran Rajagopalan wrote: > > Hi Bruce, > > > > > > Thanks very much. I will wait for Avi Synder's response. > > > > > > Thanks a lot > > Venkat > > > > > > On Sat, Jun 21, 2014 at 8:23 PM, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Venkat > > > > I'll cc Avi Snyder. Avi: do you know what this error message > > means? > > > > thanks > > Bruce > > > > > > On Sat, 21 Jun 2014, Venkateswaran Rajagopalan wrote: > > > > Dear All, > > > > I am sorry to post this again. Any help will be > > greatly appreciated. I am > > struck as I am unable to run the recon-all step. > > > > Thanks > > Venkat > > > > ---------- Forwarded message ---------- > > From: Venkateswaran Rajagopalan > > <venkateswa...@hyderabad.bits-pilani.ac.in> > > Date: Fri, Jun 20, 2014 at 5:14 PM > > Subject: mpr2mni305 failed, see > > transforms/talairach_avi.log > > To: Freesurfer support list > > <freesurfer@nmr.mgh.harvard.edu> > > > > > > Hi All, > > > > I am getting the the following error when I run > > recon-all -subjid E368 > > -autorecon1 > > > > ERROR: mpr2mni305 failed, see > > transforms/talairach_avi.log > > > > Here is what talairach_avi.log says > > > > > /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri > > /usr/local/freesurfer/bin/talairach_avi > > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > > $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp > > $ > > Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic > > #46-Ubuntu SMP Thu Apr > > 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux > > Fri Jun 20 17:06:38 IST 2014 > > mri_convert orig_nu.mgz talsrcimg.img > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > > mreuter Exp $ > > reading from orig_nu.mgz... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to talsrcimg.img... > > Analyze Output Matrix > > -1.000 0.000 0.000 129.000; > > 0.000 0.000 1.000 -129.000; > > 0.000 -1.000 0.000 122.500; > > 0.000 0.000 0.000 1.000; > > -------------------- > > INFO: set hdr.hist.orient to -1 > > mpr2mni305 talsrcimg > > Fri Jun 20 17:06:39 IST 2014 > > /usr/local/freesurfer/bin/mpr2mni305 talsrcimg > > $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ > > target=711-2C_as_mni_average_305 > > > > > --------------------------------------------------------------------- > > analyzeto4dfp talsrcimg -O0 -y > > > --------------------------------------------------------------------- > > > > $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ > > Fri Jun 20 17:06:40 2014 > > Writing: talsrcimg.4dfp.hdr > > $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks > > Exp $ > > Reading: talsrcimg.hdr > > header size 348 bytes > > hdr.dime.datatype offset=70 value=2 > > hdr.dime.bitpix offset=72 value=8 > > hdr.hist.orient offset=252 value=-1 > > dimensionality 4 > > dimensions 256 256 256 1 > > Reading: talsrcimg.img > > Writing: talsrcimg.4dfp.img > > Writing: talsrcimg.4dfp.ifh > > ifh2hdr talsrcimg -r0to255 > > ori=2 > > > > > --------------------------------------------------------------------- > > gauss_4dfp talsrcimg 1.1 > > > --------------------------------------------------------------------- > > > > $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp > > $ > > Reading: talsrcimg.4dfp.img > > Writing: talsrcimg_g11.4dfp.img > > image dimensions 256 256 256 padded to 288 288 288 > > processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 > > 10:45:03 nicks Exp $ > > Fri Jun 20 17:06:46 2014 > > Writing: talsrcimg_g11.4dfp.hdr > > > > Writing: talsrcimg_g11.4dfp.ifh > > including: talsrcimg.4dfp.img.rec in > > talsrcimg_g11.4dfp.img.rec > > > > > --------------------------------------------------------------------- > > imgreg_4dfp > /usr/local/freesurfer/average/711-2C_as_mni_average_305 none > > talsrcimg_g11 none > > talsrcimg_to_711-2C_as_mni_average_305_t4 4355 > > > --------------------------------------------------------------------- > > > > $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp > > $ > > imgreg_4dfp: > > > /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img read error > > > /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img > > 256 256 256 1 > > 1.000000 1.000000 1.000000 > > orientation T byte_order littleendian > > Reading image: > > > /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img > > dimensions: 256 256 256 > > mmppix: 1.0000 -1.0000 -1.0000 > > center: 128.0000 -129.0000 -129.0000 > > ERROR: > > 'imgreg_4dfp > /usr/local/freesurfer/average/711-2C_as_mni_average_305 > > none talsrcimg_g11 none > > talsrcimg_to_711-2C_as_mni_average_305_t4 4355' > > failed! status=255 > > ERROR: mpr2mni305 execution aborted > > > > Any help will be greatly appreciated. > > > > Thanks > > Venkat > > > > > > > > _______________________________________________ > > 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 >
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