ok, just changing the output should do. I'll try it out. thanks.
George P.
On Mon, 1 Nov 2004, Bruce Fischl wrote:
what are you trying to do? Either use a different output format, or scale your values up (e.g. in matlab)
Bruce
On Mon, 1 Nov 2004, George Papadimitriou wrote:
You are correct, my input is bfloat. Can you please offer a workaround to this issue?
Should I convert my two inputs to unsigned characters before I proceed?
Thanks, George P.
On Mon, 1 Nov 2004, Bruce Fischl wrote:
Hi George,
what is the range of values in your input (bfloat) volume? Note that COR is an 8 bit format, so if you input is floating point and <1 it will be set to 0.
cheers, Bruce
On Mon, 1 Nov 2004, George Papadimitriou wrote:
Hi all,
I'd really appreciate it if I can get some input on the issue below. I need to come up with an answer this week.
I am having some trouble with manual co-registration using tkregister2. I have placed the data in:
/space/friday/users/dtuch/tkregister2
Here is the info:
f prefix --> template s prefix --> subject to be co-registered with template s_to_f/ --> contains the co-registered result (COR)
I did the co-registration using the following command:
% tkregister2 --targ f_000.bfloat --mov s_000.bfloat --reg \ register1.dat
It worked pretty well; the only trick was that I had to click in the image window and hit 'i' to turn on the automatic intensity normalization. This process saved a new transformation matrix to the register1.dat file.
The register1.dat file was used to transform the input volume by using the mri_vol2vol command:
% mri_vol2vol --in f_000.bfloat --out s_to_f/. --interp \ trilin --temp f_000.bfloat --xfm register1.dat --invxfm
The problem is that when I try to load the result in tkmedit (or tkregister2):
tkmedit -f s_to_f
I don't see an output volume (every voxel seems to be zero)
Can you please take a look at the data when you get a chance? Please, let me know if you need me to provide additional info.
Thanks a lot! George P.
PS After you evaluate this case, if you also think I need to email the freesurfer list, just let me know.
On Wed, 27 Oct 2004, David Tuch wrote:
Hi George,
can you direct me to avg_000.bfloat ?
tnx, D
On Wed, 27 Oct 2004, George Papadimitriou wrote:
Hi Dave,
Have you run into the issue described below?
Thanks a lot! George P.
---------- Forwarded message ---------- Date: Wed, 27 Oct 2004 11:53:07 -0400 (EDT) From: George Papadimitriou georgep@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: tkregister2 question
I am trying to register a lowb volume to an average volume.
In this particular case, I'm trying to use tkregister2:
% tkregister2 --targ avg_000.bfloat --mov indivsubj_000.bfloat --reg \ register.dat
I am having a problem with the brightness of the TARG volume. It seems to be set near ~1, and using the fmov option only adjusts the brightness on the MOV volume. It is kind of hard to align them, when the target volume looks like a binary mask (appears all white). Have you seen this before?
Changing the contrast doesn't seem to help.
Thanks, George P.
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