Dear Douglas,
Thank you for your input. Additional background information to answer your
question (why not register the anatomical to the DTI):
Freesurfer segmentation was done in a previous project and used the native
space T1 scans. For this DTI project, I would like to use the Freesurfer
segmentation so I can do (amongst other analyses) ROI to ROI tracking. To be
able to use this previously segmented data, I used the native space anatomical
scans and registered them successfully to the DTI scans and continued my
analysis. Although it seems to work initially (they overlap and I can
successfully do tracking with mrtrix), it gives dimension mismatch errors later
in my pipeline. My pipeline assumes that my data is in MNI space and assumes a
specific size for the bounding box of the scans. The anatomical native scans do
not fit this criteria and my code crashes later in my pipeline. I have not been
able to work around this issue.
I would like to register a MNI T1 scan and register this to my DTI data, and
have the freesurfer output in the same space. Do I understand correctly that I
could extract a registration matrix from a realigned MNI T1 scan and then apply
this to a segmentation with mri_label2vol?
Thank you for your time and effort.
Sandra
> On 25 Jul 2016, at 17:11, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote:
>
> If you have a registration matrix that maps to the desired orientation, then
> you can apply it to a segmentation with mri_label2vol. But why not just
> register the anatomical to the DTI (bbregister) and then run mri_label2vol
> with that registration to map the WM mask directly into the native DTI space?
>
> On 7/25/16 7:56 AM, Sandra Hanekamp wrote:
>> Dear Freesurfer community,
>>
>> I would like to apply ACPC alignment to Freesurfer output.
>>
>> Data was previously segmented with recon -all and a lot of manual editing
>> using ITK. Unfortunately, the data was not aligned to ACPC and this causes
>> errors in my pipeline (I am using the labels and white matter mask from
>> Freesurfer for my DTI analysis).
>>
>> Re-doing the segmentation plus necessary edits would be very time-consuming
>> due to a poor contrast between white and grey matter and the number of scans
>> that I have, so I would prefer to align the current output to ACPC. Does
>> anyone know a solution that does not involve re-doing the segmentation? How
>> can I apply ACPC alignment to Freesurfer output?
>>
>> Thank you so much for any thoughts or recommendations you might be able to
>> provide.
>>
>> Sandra Hanekamp
>> Laboratory for Experimental Ophthalmology
>> University Medical Center Groningen
>>
>>
>>
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