what do you mean the hippocampus is left out? it is not part of the surface since it is a subcortical structure. Look at the aseg.mgz

On 12/9/2020 9:53 AM, Albulena Shaqiri wrote:

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Dear all,

I am new to freesurfer and this might be an evident question, if so, I am sorry.

We have a longitudinal study with t0 and t1 scans. I followed the procedure and did the 3 steps.

1. Cross (with the following command: recon-all -subject 01_t0 -i /subjectfiles/t0/sanlm_13.nii -all -qcache -notal-check)

2. Base (recon-all -base 01_t0t1template -tp 01_t0 -tp 01_t1 -all)

3. Long (recon-all -long 01_t0 01_t0t1template -all)

The problem is once I am inspecting the data, I see that the hippocampus is left out in all the cases (4 different subjects are attached in the screen captures).I used this command: freeview -v 01_t0/mri/norm.mgz \ -f 01_t0/surf/lh.pial:edgecolor=red \ 01_t0/surf/rh.pial:edgecolor=red \ 01_t0/surf/lh.white:edgecolor=blue \ 01_t0/surf/rh.white:edgecolor=blue)

Also, you should know that we used for T1 MP2RAGE instead of MPRAGE.

Is there anything I can do without having to re-do all the corrections by hand point by point and without having to restart over all my data pre-processing?

I have to specify that we are interested in the hippocampus, so this is a major point in our study.

Thanks in advance for your help,

Alba

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