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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Can you chmod those files? I don't have read perms to all of it.

What are you trying to do? Resample f to s or s to f?

doug

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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer