External Email - Use Caution Thanks for pointing that out. The step numbers are those from section 5 in https://secure-web.cisco.com/1MvjYJiIaIHWh8caycAJQMG2vD_09oIjJWD1kFpdpLGaLJqKUqv6siDUfatz8I9fZHcEbD5srsIxxiiVUpuAOzYLar0k7ybBjxcILafPvtIOZQBLhepP2-e7M1gXLLaFz7Bz1uYH_2RNmKyJQkjr37qjFktM2vJ8vEWfezVqXEXwLSxz5me_DbfOe-QHIa1mk1R2VcONTJmlksUV_MZ3WWWDmfygwDwbfgp4yc7Ov-plyxj7Cp588_xW9WlLhU8nCsgBUwn2nXZt1lUnef0TSGRw-JOoHLhhqSje17kZado6G5wW0_uQ3JXHTw-h33lfI/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all
On Tue, Aug 30, 2022, 6:16 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > There is not enough information to understand what you did in #2 > > On 8/30/2022 3:56 PM, Ruifeng Dong wrote: > > External Email - Use Caution > Hi all, > > I am computing volumetry using freesurfer using two different runs. > > 1. I just use recon-all -all, and then look at the aseg.stats file. > > 2. I ran recon-all only to the 12th step where gca labeling is done. It > doesn't generate the aseg.mgz file but only aseg.auto.mgz. I assumed that > they are the same and ran the -asegstats step to get the output in > aseg.stats. > > I noticed there are differences between the above two runs on the same > image. Firstly, the volumes of WM, GM and ICV are not there from the 2nd > run. How does this happen? In which step does Freesurfer compute these? > > Secondly, the volumes of some subcortical structures are also different > between the two runs. Does Freesurfer make corrections to the volume > segmentations after step 12? > > Thank you! > > Ruifeng > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1nbDpNGhlO8S2mJqYzslOHhceoHNXymcQ5InPEtzkoaBHTmUBGFLBD0ftaxiBU3tZkgnBpMy_IGdO6lArLUFflzQP2z3-oRPeQTlETipTpoK-Dp8_KESVbBzcg8Pog_XExCqI38lilJ26XBdDyVd68ZVEW66RM_L_VpycfK8PUrLMg3dWoALMYsr7AcdAZGPMQIe30zx6Ig3MnFWbK-kEfQZYtEr3b7YfBxDvbnT6FPnlST-hHPScWDEsvN5fMaIcOlybWu14u9NFPW1Z8ENbNIKkv87kAZT-R0X0TuF0YQSJM9FYfnRqoclU_UA1b6Y3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/16W4w5rco4KczASit5D4JyFZruG-ABKPiMhwl1p6RWW53SGnYLCVcq_uOmwEeO6B_AQf1SCNQmxVUj38gPUI7ombGc5QfSBlkUPh-ZncRh-1oG3l-5YYloMY8VW611KI4ka9KgwCrekqn67UlAottbvWN7JJWwFihuanBiYHFJO191uDhHefbGOaOytBixGGnyyYZUV_LjIwScz5GnOl7cqX8P_0Rb9o2_fadn52sqI5vhfKmT6SkWXIQGLRD8KkFpITkL7bE1ZDTmSMCeeEwh4K0uxs2-NDF7FjSECHi3HcIFbFat3CvD78VpNOuEDR_/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/16W4w5rco4KczASit5D4JyFZruG-ABKPiMhwl1p6RWW53SGnYLCVcq_uOmwEeO6B_AQf1SCNQmxVUj38gPUI7ombGc5QfSBlkUPh-ZncRh-1oG3l-5YYloMY8VW611KI4ka9KgwCrekqn67UlAottbvWN7JJWwFihuanBiYHFJO191uDhHefbGOaOytBixGGnyyYZUV_LjIwScz5GnOl7cqX8P_0Rb9o2_fadn52sqI5vhfKmT6SkWXIQGLRD8KkFpITkL7bE1ZDTmSMCeeEwh4K0uxs2-NDF7FjSECHi3HcIFbFat3CvD78VpNOuEDR_/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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