There would be a lot more (if running to the end). You can look at the recon-all.cmd file for a list of commands in the order that they are run

On 3/18/2021 4:19 PM, Jaiashre Sridhar wrote:

External Email - Use Caution

Hello,

I am using FreeSurfer version v7.1.1. For few subjects who have already been through the complete recon-all pipeline, I would like to re-run the recon steps downstream of “-fill”. I am using the following commands to do so. Can an expert check and let me know if this encompasses all the downstream steps accurately for v7.1.1?

/### Recon commands begin ###/

/re//co//n-all -s [subjid] -tessellate -smooth1 -inflate1 -qsphere -fix///

//

/cd [subdir]/mri///

//

/#--------------------------------------------///

/#@# AutoDetGWStats lh / //

/mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh///

/#--------------------------------------------///

/#@# AutoDetGWStats rh / //

/mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh///

/#--------------------------------------------///

/#@# WhitePreAparc lh / //

/mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5///

/#--------------------------------------------///

/#@# WhitePreAparc rh / //

/mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5///

/#--------------------------------------------///

/#@# CortexLabel lh ///

/mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label///

/#--------------------------------------------///

/#@# CortexLabel+HipAmyg lh ///

/mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label///

/#--------------------------------------------///

/#@# CortexLabel rh ///

/mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label///

/#--------------------------------------------///

/#@# CortexLabel+HipAmyg rh ///

/mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label///

//

/recon-all -s [subjid] -smooth2 -inflate2 -curvHK -autorecon3///

/### Recon commands end ###///

Additional question – Is there an individual flag that replaces the hardcoded commands above for AutoDetGWStats, CortexLabel, WhitePreAparc and CortexLabel+HipAmyg?According to the [subjid]/scripts/recon-all.cmd file, I see that these additional commands are added to v7.1.1 but are not present in the recon steps listed here for stable 7.1.1 release *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 https://secure-web.cisco.com/1mh5NrCnQZwjol6BqUWZ3zVU1wUDX0ceM5QaWcfAsgmEUHYk00OqTCzkRJ8ZxyfxHBKvg2i5eXk16yX4zKqHKr-d-tEnket_QAspom0sMcjBfRUcMFJ9MEL445wThQ2-zD1acrLdUCLAkh89aW4nZxGrInunXHDdjGj0hgJiJsQnRLVThTH5AN35m-SF_C6gdBFLHGG7LLaExnHcuPqmLEc91foPb9aJGLxmyasGT7n1i4A2KhDe10D9nQg_wQtCpvHqfP2Xb4Gp-ADXn9WRykg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0.

Thank you in advance for your response.

Sincerely,

Jaiashre.

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