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Hello everyone,
I hope you can help me with my little problem I encountered after manually editing the skull strip. Because my internet provider crashed I'm unable to upload the log file right now and writing this from my phone.
For context: I'm analyzing data with freesurfer 6.0 because the data sets already went through the recon-all process some months ago with freesurfer 6.0. I just got the data sets and my first step was to manually edit bad skull strips using tkmedit. This worked fine but after I finished and saved the data set I wanted to run: recon-all -autorecon-pial -subjid P_01
This stopped with errors and at the bott of the log i found this note which probably led to the crash: MghRead(/usr/local/freesurfer/subjects/P_01/MRI/../MRI/asset.presurf.mgz, -1): could not open file
I looked into the folder and can't even find this file. Did I miss a step I have to do before or can this be due to getting the data after running recon-all on a different PC?
My pre-processing pipeline looks like this (keep in mind I already get the data after recon-all was completed): 1. Skull Strip (either manually or using gcut depending on data quality) 2. Checking surfaces visually and talairach transforms if needed 3. White matter intensity normalization.
Do I need to change the order here or am I missing something completely? I'm new to freesurfer and have to get into it myself. The broad tutorials online help but it's hard to check what I have to do in which order and how. If you have other guides I can check this would be an incredible help.
Thanks for the help and sorry for the long email, I really appreciate every tip.
Best regards,
Nils