[MINC-users] Strange problem with mritoself

[Jason Lerch]

Try either
mritoself -nothreshold
or
mritoself -threshold <args>

and rerun it on your old images. Mritoself is dying at the automatic 
thresholding stage, which is often unnecessary for getting a good fit.

Cheers,

Jason

Thomas Mansi wrote:

>Dear all,
>
>I'm using mni_autoreg0.98r and I'm having a very strange problem. Maybe
>you could help me.
>
>I want to coregister a T2 axial MRI to a T1 MRI (intrasubject), by doing
>the following:
>
>$ mritoself -lsq9 -mi -far -clobber \
>-model icbm_avg_152_t1_tal_lin_symmetric \
>-modeldir /usr/local/mni/data/models/ \
>-mask target -target_talxfm xfms/patient_t1_to_tal.xfm \
>proc/patient_t2ax_clamp.mnc.gz \
>proc/patient_t1_clamp.mnc.gz \
>xfms/patient_t2ax_to_t1.xfm
>
>However, though this command works with our newly acquired (and
>isotropic) MRI (from the Siemens machine), I get the following error on
>some older anisotropic images:
>
>[mritoself] [mansi at Toshiba:/cygdrive/e/Documents/NOEL/temp/FCD-mspec]
>[2006-03-28 19:44:45] /usr/local/mni/bin/minctracc -clobber
>/tmp/mritoself_3804/patient_t2ax_clamp_crop.mnc
>/tmp/mritoself_3804/patient_t1_clamp_crop.mnc
>/tmp/mritoself_3804/patient_t2ax_to_t1_tmp1.xfm -est_center
>-est_translations -lsq9 -mi -groups 256 -threshold 100 0 -model_mask
>/tmp/mritoself_3804/patient_t1_clamp_mask.mnc -step 7.3 7.3 7.3 -simplex 10
>COG of v1: -0.076698 28.486593 23.346405
>COG of v2: 0.285103 16.833281 29.833879
>   [trans] = 0.361800 -11.653313 6.487474
>Only center & trans required, now returning from init_transformation
>slice lim 17 0
>row lim   32 0
>col lim   32 0
>thresh =  100.00000    0.00000
>No voxels were found in volume 1 with value above threshold (100.000000).
>Error in /usr/local/mni/bin/minctracc in file init_lattice.c, line 545
>Cannot calculate size of volume 1
>.mritoself: crashed while running minctracc (exit status=65280)
>
>I don't really understand what's going on here. The source MRI are first
>nu-corrected using N3 (nu_correct patient_t2ax.mnc patient_t2ax_nuc.mnc)
>and then clamped (grey level intensities clamped between 0 and 100). Of
>course, the target T1 MRI has already been coregistered to Talairach
>space. Minctracc seems to invert the min/max intensity values ...
>
>The problem happens on my Cygwin system (laptop with windows XP) but
>also on Linux and SGI machines. It seems to be related to the input
>images, since the program works very well with recent volumes and some
>oldest ones, but fails with others... Did I miss something? Must I
>upgrade my mni_autoreg?
>
>Many thanks in advance for your help!
>
>Best regards,
>Thomas Mansi
>
>
>	
>
>	
>		
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