yeah, I know. That's Doug vs. me (you can always tell the difference
based on whether the help is useful (Doug) or not (me)).
sorry,
Bruce
On Mon, 26 Jun
2006, Sebastian Moeller wrote:
Hi Bruce,
On 26. Jun 2006, at 16:49 Uhr, Bruce Fischl wrote:
yeah, sorry, that's on our list of things to fix.
This will make a great tool even greater, thnanks. Then again, for
the smaller monkey brains the "fake the resolution to be 1mm isotropic" does
the trick nicely, once you know it, that is ;).
I just added a --conform to mri_info so that it will return "yes" or "no"
(also --type). Will be live in dev tomorrow. Nick: does the dev build go on
the web every day?
Waoh, how cool, thanks a million. Just a nit, mri_normalize uses "-u"
to get to the help while other fs tools use either "-h" or gnuish "--help",
maybe you might want to consider to consolidate to one uniform command line
switch? But I digress...
ahoi
Sebastian
Bruce
On Mon, 26 Jun 2006, Sebastian Moeller wrote:
Hi Bruce,
On 26. Jun 2006, at 16:15 Uhr, Bruce Fischl wrote:
it should - consider it a bug.
On a related note, is there an easy way to convince mri_info to just
spit out the type (UCHAR FLOAT etc.) so I can easily script whether the
conform step is necessary or not (instead of making the temporary file ->
grep gymnastics ;)).
Have you tried mri_convert -cm (conform to min)? That will make it 8 bit
and isotropic, but at the highest linear resolution it finds. I think
that's what people here use when they're doing monkey recons.
Ah, I just use "-iis 1 -ijs 1 -iks 1" to fake the right resolution (I
do scan at .5 mm isotropic), that way I get nice large dislayes volumes in
tkmedit/tkregister2. With the large displays it is very easy to do the
manual rotations to get the AC-PC line horizontal and adjust rotations
around the other two axis. I will try "-cm" if that also gives a "full
size" display in the visualizers, I will switch.
Just checked it, tkmedit silently drops every other slice (at least
in the display), so this will not be very satisfactory for the three
manual steps (cleaning the brainmask, distributing shiploads of control
points, and getting the wm.mgz into good shape). So unfortunatelly, I will
have to stick to cheating about the resolution :(.
Ahoi & thanks
Sebastian
Bruce
On Mon, 26 Jun 2006, Sebastian Moeller wrote:
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
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