Hi Bruce,
On 26. Jun 2006, at 02:30 Uhr, Bruce Fischl wrote:
Hi Sebastian,
why do you want to run mri_normalize on non-conformed volumes? It
wasn't really built for it.
Well I have monkey data, which I feed into freesurfer, so only few of
the automatic step actually work for me. Therefore I do call all the
relevant programs/scripts by hand. Until now I used freesurfers
skull-strip (which feeds on the fully conformed T1 volume)
Now, to be able to use fsl's BET, I spatially conforme the input just
after making sure that its orientation is right (this is the rawavg.mgz
volume, of type float). And to give BET something to feed from I would
rather not lower rawavg.mgz's resolution to 8bit just yet, given that
the scans have 11bit resolution. I do admit that those 3bit probably
are in the noise though ;).
So all I am reporting here, is that mri_normalize's "-conform"
argument does not go the full mile, but only seems to consider the
spatial part of conforming (which is not obvious from the output of
"mri_normalize -u", I thought interpolation would also cover the
process of 32 to 8 bit conversion).
Ahoi
Sebastian
Bruce
On Sun, 25 Jun 2006, Sebastian Moeller wrote:
Hi List,
as the subject line says I am having problems running mri_normalize
(on suse 9.3 x86_64, freesurfer centos4 x86_64 3.0.2 release). When
feeding in slightly unconformed volumes (like 1mm isotropic 256 by
256 by 256 of type 3 (float)) mri_normalize's "-conform" argument
fails (fully unconformed volumes are no problem). The error message
boils down to MRInormGentlyFindControlPoints: unsupported src format
3" followed by "MRI3dGentleNormalize failure! mri_ctrl=Null".
I just work around this by running a full mri_convert --conform on
my input file before running mri_normalize. Just a nit, specifying
"-v" some where else than at the end of the commandline easily
produces segmentation faults (probably because -v is "overloaded" to
also expect Gx Gy Gz arguments? the help is a bit terse)
Ahoi
Sebastian
--
Sebastian Moeller
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Institut fuer Hirnforschung III
Abteilung Theoretische Neurobiologie
Universitaet Bremen
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