what does the rawavg.mgz look like? If it is ok, can you email it to us? On Fri, 8 Aug 2014, Francesco Deleo wrote:
Thank you all for attention and help! Maybe we're finding the problem: in cases I received the mpr2mni305 error the orig.mgz is unintelligible (it is white with some black point). But my dicoms are ok (I've checked!). I've already tried converting dicom to tiff but I got the same error message and the same unintelligible orig.mgz (and the tiff are ok too!). So I think the likely problem is in the recon-all -i command! Any idea?
It remains a mistery for me why I have this problem only in some (and not in every one) MRI scans even if all the parameters are the same.
thanks again
Francesco
2014-08-07 17:16 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu: Have you looked in transforms/talairach_avi.log?
On 08/07/2014 07:57 AM, Francesco Deleo wrote: > Thank you Doug! > but i tried it in many cases but I've always received the same error > message... > Is there something else I can try? > > Francesco > > > 2014-08-07 0:46 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>:
Try it with -notal-check doug
On 08/06/2014 04:39 PM, Francesco Deleo wrote: > I all! > > I am a new freesurfer user. > I have a problem when I perform the recon-all -all, in about
15% of
> MRI scans, all made with the same scanning protocol (T1 MPRAGE
in a
> SIEMENS Avanto 1,5 T). > > I can't recognize any difference between those scans which
work
> correctly and those not. > I have never found the same error on 3T MRI scans. > > I've already tried to add these flags to the recon-all -all
command:
> -use-mritotal > -talairach -use-mritotal > -notalairach > but I've always received an error message > > Thank you very much > > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log > Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version 13.3.0: > Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 > > Thanks very much for your attention > > Francesco > Milan, Italy > >
> > FREESURFER_HOME: /Applications/freesurfer > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > Kernel info: Darwin 13.3.0 x86_64 > >
> > > LAST LINES IN TALAIRACH_AVI.LOG > > parameters > 9.0270 134.9373 110.8627 -84.3566 -7.5458 -11.3475 > eta,q 0.95791 3.72402 > 0.0485 0.0470 0.0477 0.0513 0.0470 0.0452 > 0.0475 0.0471 0.0478 0.0513 0.0457 0.0435 > 0.0472 0.0472 0.0476 0.0428 0.0434 0.0415 > 0.0471 0.0471 0.0476 0.0435 0.0430 0.0415 > 0.0470 0.0478 0.0457 0.0525 0.0415 0.0430 > 0.0473 0.0511 0.0430 0.0548 0.0442 0.0453 > 0.0486 0.0426 0.0406 0.0672 0.0431 0.0503 > niter,ni,del,rscale 7 3 12.0000 1.2000 > imgrege: no voxels in register > ERROR: 'imgreg_4dfp > /Applications/freesurfer/average/711-2C_as_mni_average_305 >
/Applications/freesurfer/average/711-2B_as_mni_average_305_mask
> talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4
1283'
> failed! status=254 > ERROR: mpr2mni305 execution aborted > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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