Hi Francesco
if you upload one of the dicom series that causes the problems we will
take a look. If you can also send us the rawavg.mgz after your successful
recon-all from the .nii that would also help
cheers
Bruce
On Wed, 20 Aug 2014, Francesco
Deleo wrote:
Hi all!
Sorry for my late answer but I went on holiday and I didn't have access to
my mail.
The background is normal in original dicoms and it is not an avarage of more
than one run.
The problem I reported was solved in all cases converting dicoms to nifti
with dcm2nii and using the oriented volume. I don't know why but it
functioned
Is there a bug in freesurfer using directly dicoms?
Thank you all for attention and advice.
Francesco
2014-08-08 19:53 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
can you tar and gzip the dicoms and send them to us? Is there a
high background level in them as well? Is this the average of
more than one run? You should check the mri/orig/00?.mgz
volume(s) as well
On Fri, 8 Aug 2014, Francesco Deleo wrote:
---------- Forwarded message ----------
From: Francesco Deleo <franc.de...@gmail.com>
Date: 2014-08-08 18:06 GMT+02:00
Subject: Re: [Freesurfer] mpr2mni305 failed error
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
It is not ok...
It seems to have a contrast problem... I can send a
snapshot, or if you want
I can send the rawavg.mgz
Francesco
2014-08-08 17:53 GMT+02:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
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
<gr...@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
<gr...@nmr.mgh.harvard.edu
> <mailto:gr...@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
> >
> >
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
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>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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