Hi Doug,

I tried running mri_vol2vol again (after you made the changes); the good news is that as you said the output is not zero, but at the same time the output volume is definitely not correct (the brain appears stretched, and not in register with the template). From what I can gather, you also tried this in:

/space/friday/users/dtuch/tkregister2/s_to_f-dng

I also tried a suggestion that Bruce had made earlier (i.e. specifying the output to be a bfloat volume, instead of COR), but it yielded the same result (output appears stretched and not in register).

I would really appreciate your help resolving this issue.

Thanks, George P.

On Mon, 1 Nov 2004, Doug Greve wrote:

OK, mri_vol2vol should give non-zero output now. I have not looked at it closely enough to tell whether your actually doing what you want to do.

doug

George Papadimitriou wrote:

...

OK, I changed the permissions. I am trying to co-register s to f.

George P.

On Mon, 1 Nov 2004, Doug Greve wrote:

...

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:

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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:

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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

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422