Dear experts,
I am trying to use T2-weighted images (0.5x0.5x1mm) as an additional scan to a T1-weighted image (0.7x0.7x0.7mm) for hippocampal subfield segmentation in Freesurfer 6. The T2-weighted data is a slab which includes the whole hippocampus and its y-axis is parallel to the hippocampal long axis (image dimensions [384,384,50]). When I try to use recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>I always get a faulty alignment (through visual inspection by overlaying T2.FSspace.mgz on T1.mgz in freeview or by looking at the quality control image T1_to_T2.v10.QC.gif), even when I manually align the images beforehand.
Do you have any idea or hint how to improve the registration and thus start the segmentation correctly? I also tried to find out which registration tool is used for this (mri_robust_register?) in order to play around with it and would also be thankful for any hint on this.
Thank you for your advice and time,
Best,
Frauke
What version of FS are you using? Can you send the recon-all.log file?
On 7/3/17 4:35 AM, Frauke Beyer wrote:
Dear experts,
I am trying to use T2-weighted images (0.5x0.5x1mm) as an additional scan to a T1-weighted image (0.7x0.7x0.7mm) for hippocampal subfield segmentation in Freesurfer 6. The T2-weighted data is a slab which includes the whole hippocampus and its y-axis is parallel to the hippocampal long axis (image dimensions [384,384,50]). When I try to use recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>I always get a faulty alignment (through visual inspection by overlaying T2.FSspace.mgz on T1.mgz in freeview or by looking at the quality control image T1_to_T2.v10.QC.gif), even when I manually align the images beforehand.
Do you have any idea or hint how to improve the registration and thus start the segmentation correctly? I also tried to find out which registration tool is used for this (mri_robust_register?) in order to play around with it and would also be thankful for any hint on this.
Thank you for your advice and time,
Best,
Frauke
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Frauke Beyer