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Dear Freesurfer experts,
I ran recon-all on 100 subjects. Around 20 of them needed manual corrections of the pial surface on the brainmask.mgz. 1.) Can I run the command: "recon-all -make all- s <subject>" on all 100 subjects and it will only recon-all the manually edited ones or do I need to run it individually for the 20 subjects? 2.) Do I need to add the flags which I used for the original recon-all command to the "recon-all -make all- s <subject>, e.g. -qcache -T3 -hippocampal subfields etc?
Many thanks!
/Ben
On 2/11/2020 9:26 AM, Benjamin Ineichen wrote:
External Email - Use Caution
Dear Freesurfer experts,
I ran recon-all on 100 subjects. Around 20 of them needed manual corrections of the pial surface on the brainmask.mgz. 1.) Can I run the command: "recon-all -make all- s <subject>" on all 100 subjects and it will only recon-all the manually edited ones or do I need to run it individually for the 20 subjects?
It might work, but the "make" function has always been a little unreliable (and probably won't be in the next version)
2.) Do I need to add the flags which I used for the original recon-all command to the "recon-all -make all- s <subject>, e.g. -qcache -T3 -hippocampal subfields etc?
Yes
Many thanks!
/Ben
-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto:ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto:ineichen@protonmail.ch +41 76 391 04 01
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