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