our pleasure (most of the time)
On Thu, 29 Jun 2006, Sebastian Moeller
wrote:
Hi Nick, hi Bruce,
On 29. Jun 2006, at 00:39 Uhr, Nick Schmansky wrote:
The dev build is not posted on the web anymore, rather, bug fixes and
tested minor enhancements get folded into the stable build and released
periodically (so far, it seems about every six weeks).
Which, I might add, is really great. Then again, if you want me to
test anything I'd be happy to do so.
A new stable release (v3.0.4) will be forthcoming, and I'll make sure
that the --conform flag of mri_info gets included.
Great.
Ahoi & thanks for all the fish, ermh, the nice tools & the great support
Sebastian
On Mon, 2006-06-26 at 10:49 -0400, Bruce Fischl wrote:
yeah, sorry, that's on our list of things to fix.
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?
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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