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Dear FreeSurfer experts,
I have a question regarding manual edits and change of FreeSurfer version.
In our lab, we have thus far processed most of our T1 scans using FS version 5.1 and have performed manual edits when needed. We are now updating our processing to FS version 6.0, and would like to use previously edited data (from the 5.1 version) as an input for the FS version 6.0 processing (based on previous emails from the mail archive, I understand this makes sense?).
Ideally, I'd like to store the FS6 outputs in a new parent directory (different from the directory where the FS5.1 processing outputs are stored). However, simply running:
recon-all -s subject_name -sd /path/to/FS6_outputs/ -all
... with /path/to/FS5.1_outputs/ as a SUBJECTS_DIR doesn't work (it looks for input data in the -sd specified output directory, which doesn't contain anything yet).
Adding an -i flag with a full path to the desired output directory also doesn't work:
recon-all -s subject_name_FS6 -sd /path/to/FS6_outputs/ -i /path/to/FS5.1_outputs/subject_name/
... as it says the -i flag needs a file as an input, not a folder.
Now, adding an -i flag and giving for instance the 001.mgz as input works:
recon-all -s subject_name_FS6 -sd /path/to/FS6_outputs/ -i /path/to/FS5.1_outputs/subject_name/mri/001.mgz
However, if I am not mistaken, the manual edits are not stored in this 001.mgz file. Thus, does this mean that when rerunning a new version of freesurfer on already processed data, the same subject folder has to be used as input (FS 5.1 processed data) and output (FS 6 processing outputs)?
And if so, should old files (that remain non-modified after the FS6 run) be removed?
Thank you in advance for your answer,
Best regards,
Joëlle van der Molen