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
Hi Joao,
Sorry for the late response, but I've been away for two weeks ...
When recon-all is first run (and there is not talairach.xfm), it will
create talairach.auto.xfm and copy that to talairach.xfm. In subsequent
runs, recon-all will create a new talairach.auto.xfm. Immediately prior
to t
These are computed and saved in subject/stats in text files
?h.aparc.stats and aseg.stats. For aseg.stats, the volumes are in cubic
mm. aparc.stats reports both surface area (mm^2) and volume (mm^3). If
you havea bunch of subjects and you want to create a spreadsheet, you
can use asegstats2ta
Hi Lars,
sorry for the late response, I've been gone for two weeks.
Qs 1and 2: Did you look at mri_glmfit --help? It describes what all
these things are. You can also look at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis.
Q3: If you are loading a surface-based overlay,
Use the method that Kevin described to get a label. Then use
mri_vol2roi on the FSL stat volume to get a text summary.
doug
Joongnam Yang wrote:
Thanks, Bruce & Kevin,
What I meant is that
1. I have an overlay image (FSL functional image overlaid onto
Freesurfer inflated image). So, th
it should - consider it a bug. 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.
Bruce
On Mon, 26 Jun 2006, Sebastian Moeller wrote:
Hi
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 te
reg-feat2anat uses brain.mgz. But you'll have to give us more detail in
order to evaluate the problem, "somewhat inaccurate" is not very
informative. Please give cmd lines, versions, and log files.
reg-feat2anat does use flirt, and it will print out the flirt cmd line.
You can compare it to t
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.
Thanks Reza, that's just what I would have said!
Reza Rajimehr wrote:
This is Doug's response to my question. It might be also relevant to your
question.
Reza
**
Not directly. tkmedit is a volume viewer, and the spherical maps are of
cour
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, t
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 t
Is the format the same as the xfm files? I thought .mnc meant that it
was a volume. If you have an xfm file that maps from functional to the
freesurfer anatomical, then you can do something like:
tkregister2 --mov func.mnc --xfm your.xfm --s yoursubjectname --reg
register.dat
doug
Jer
Hey all,
I was wondering if anyone knows the format for the Talairach.bnd file?
Specifically what I am looking for is what the matrix at the bottom actually
represents. I am going to use them in a script to actually trim the brain so I
need a way to compute the 6 planes that make up the box a
HI Sebastian,
I made a mod to this in development version, but it operates slightly
differently in that you set the "nth" run with -run. Eg, -run 2 would
mean to use the 2nd run. Otherwise, if you run it on more than one
session, the run that you specify might not exist. Would this work for y
Hi Doug,
On 26. Jun 2006, at 21:19 Uhr, Doug Greve wrote:
HI Sebastian,
I made a mod to this in development version, but it operates slightly
differently in that you set the "nth" run with -run. Eg, -run 2 would
mean to use the 2nd run. Otherwise, if you run it on more than one
session, th
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