On Mon, Jun 23, 2014 at 11:42 PM, Nick Schmansky, MGH <nicks@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
> <fischl@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
> <venkateswaran@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
>
>
>
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