Why are you using --no-resample? This will keep the anatomical in the
256^3 space (it just changes the header).
doug
Hansen, Kathleen (NIH/NIMH) [F] wrote:
> Thanks. The tkregister2 check gives some new information. The initial
> registration is not very bad when checked in tkregister2. Also, the final
> registration is perfectly acceptable when checked in tkregister2, so my
> original question needs clarification.
>
> What I want to do is to use the register.dat file to create an anatomical
> registered to a functional. I want the actual registered anatomical data as
> a saved file. In the past, I applied these lines to a dataset that didn't
> produce the G-W contrast warning. Also, this fmri dataset was collected in
> the same scan session as the anatomical.
> bbregister --mov epi.template_{$S}.nii --bold --s {$S} --init-fsl --reg
> register_{$S}.dat
> mri_vol2vol --reg register_{$S}.dat --mov epi.template_{$S}.nii --fstarg
> --inv --no-resample --o {$S}_Anat_in_Func_noresamp.nii
>
> The output, {$S}_Anat_in_Func_noresamp.nii, aligned well with the fmri volume
> epi.template_{$S}.nii with no other registration needed.
>
> Now I am applying these lines to several different datasets. All of them do
> produce the G-W contrast warning, and they were not collected in the same
> scan sessions as their surface anatomicals. In each case, the output,
> {$S}_Anat_in_Func_noresamp.nii, is very far from the fmri volume
> epi.template_{$S}.nii. This is strange, since in these same datasets the
> register_{$S}.dat produces a good alignment between epi.template_{$S}.nii and
> {$S}/mri/orig.mgz when viewed in tkregister2.
>
> Thanks very much for your help on this,
> Kathleen
>
> On 8/20/10 11:32 AM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote:
>
> That warning in and of itself is not critical, but it does suggest that
> the initial registration failed. I assume the registration still looks
> bad? Does this happen on a bunch of data sets or just this one? There
> are a couple of more steps. First, you can run with --init-fsl and check
> the initial registration to verify that it is way off. To do this, run
> with --init-reg-out and check that registration with tkregister2. If
> that is bad, you can can try two things. First, if you have spm and
> matlab, you can use --init-spm. Second, you can tweak the initial
> registration by hand to get it "close" (ie, within 5mm and 5deg), then
> use --init-reg
>
> doug
>
> Hansen, Kathleen (NIH/NIMH) [F] wrote:
>
>> Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it
>> was not acquired at the same time as the anatomical. Just for the heck of
>> it I tried substituting --init-header for --init-fsl anyway, and got the
>> same warning about negative G-W contrast.
>>
>> -Kathleen
>>
>>
>> On 8/19/10 2:39 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:
>>
>> It may have been the initialization that failed. Was the epi acquired
>> at the same time as the anatomical? If so, you might be able to run it
>> with --init-header. Also, is this whole brain or partial field of view?
>>
>> doug
>>
>> On 8/19/10 1:50 PM, Hansen, Kathleen (NIH/NIMH) [F] wrote:
>>
>>
>>> Hello,
>>>
>>> The following command has produced a very wrong registration and a warning:
>>>
>>> bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06
>>> --init-fsl --reg register.strange_G-W_contrast.dat
>>> ****
>>> WARNING: initial G-W contrast is negative, but expecting positive.
>>> If the mov data has a T1 contrast, re-run with --T1
>>> ****
>>> The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not
>>> T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume.
>>> Any ideas?
>>>
>>> Thank you,
>>> Kathleen
>>>
>>>
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>>>
>>>
>>>
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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