[Freesurfer] Recon-all {Disarmed}

Hi experts, I am using FS 6.0 for LGI. My data is fetal images. I ran "recon-all" pipeline for cotical thickness and LGI. Is it suitable? Or are the results reliable, such as the LGI value of precental? I am looking forward to your reply. Thank you very much. Sincerely, Zheng | | 郑凤莲 邮箱：zhengf

Re: [Freesurfer] RECON-ALL {Disarmed}

Hi Zheng can you please include the full command you ran, the full screen output and the recon-all.log file? cheers Bruce On Fri, 9 Mar 2018, 郑凤莲 wrote: Hi experts, I am using FS 6.0 to calculate LGI. But when l ran recon-all, there is an error: couldn't find DWI parameters. I don't know

[Freesurfer] RECON-ALL {Disarmed}

Hi experts, I am using FS 6.0 to calculate LGI. But when l ran recon-all, there is an error: couldn't find DWI parameters. I don't know how to resolve this problem. Looking forward to your reply. Thanks very much. Sincerely, Zheng | | 13181786167 邮箱：13181786...@163.com | 签名由 网易邮箱大师 定制___

Re: [Freesurfer] Freesurfer Recon all {Disarmed}

Hi Bruce, This is the sequence details: - Axial FLAIR: Plane=AXIAL; Acquisition Type=2D; Coil=8HRBRAIN; Field Strength=3.0 tesla; Flip Angle=90.0 degree; Manufacturer=GE MEDICAL SYSTEMS; Matrix X=256.0 pixels; Matrix Y=256.0 pixels; Matrix Z=42.0 ; Mfg Model=Signa HDxt; Pixel Spacing X=0.8593999

Re: [Freesurfer] Freesurfer Recon all {Disarmed}

and can you give us details of your FLAIR acquisition? What are the voxel sizes? What sequence? On Tue, 20 Feb 2018, Shim Hee Youn wrote: > Hi Bruce, > > Thanks for your email. I am using Freesurfer version 6 and the command I > used to run is this: > > qsub -m n -o o -e e -V recon-all -subjid ${

Re: [Freesurfer] Freesurfer Recon all {Disarmed}

Hi Bruce, Thanks for your email. I am using Freesurfer version 6 and the command I used to run is this: qsub -m n -o o -e e -V recon-all -subjid ${Z}_${Image}_fs -i ${step1LocalDir}/$T1 -FLAIR ${step1LocalDir}/${FLAIR} -FLAIRpial -all Best Regards, Shim Hee Youn Research Assistant Multimodal N

Re: [Freesurfer] Freesurfer Recon all {Disarmed}

Hi Shim Hee we need to know what commands you ran, the full screen output from them, and what version of FS you are using (at least!) cheers Bruce On Mon, 19 Feb 2018, Shim Hee Youn wrote: Hi Freesurfer team, I am currently using ADNI dataset to run Freesurfer  Recon all for MPRAGE, SPGR