Re: [Freesurfer] Error in longitudinal pipeline {Disarmed}

External Email - Use Caution Dear FreeSurfer experts Just a gentle reminder! Please do help me to resolve this issue. With regards Korann On Thu, Nov 19, 2020 at 11:54 AM vittal korann wrote: > Dear FreeSurfer experts > > This is just a gentle reminder for my query! > Looking

[Freesurfer] Fwd: Error in longitudinal pipeline {Disarmed}

External Email - Use Caution Hi FreeSurfer experts Recently I started working on the longitudinal data. I followed the pipeline described in the below link. Also, I attached my longitudinal table along with freesurfer data. https://secure-web.cisco.com/10GeKQWbNwmdQQgtn3lkt2V_V6C

Re: [Freesurfer] Mean thickness estimation {Disarmed}

External Email - Use Caution Hi Bruce, No, I don’t think that you’ve misunderstood. I was asking about cohorts that had not been visually inspected in my first message and then in my last message I wanted to check that I didn’t need to also remove people from visually inspected da

[Freesurfer] PETSURFER for AV1451

External Email - Use Caution Hi PETSURFERs,  A quick question to the group: Does any one have experience using PETSURFER on dynamic AV1451 scans? How can I know whether the MRTM1 or MRTM2 using midbrains (due to off target AV1451 binding) is suitable for my data?  Thank you! Best

[Freesurfer] Time required to run permutations

External Email - Use Caution Dear FS team, Does anyone have any idea how long does the permutation computation to handle multiple comparisons take on a surface based analysis? The command is given below: mri_glmfit-sim --glmdir rh.project.glmdir --perm 1000 3 abs --cwp 0.05 -

Re: [Freesurfer] Mean thickness estimation {Disarmed}

Hi Stephanie I see. Yes, I guess this is ok, you just want to be careful when tossing datasets that you aren’t biasing your results. Always better to look at them if you can. Big errors are pretty obvious and can be found quite rapidly (e.g. by zipping through a bunch of snapshots with nmovie_q

[Freesurfer] PETSurfer

External Email - Use Caution Dear all, How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean intensity using PETSufer? Is there a command to use in mri_gtmpvc like --rescale X? I know that I can find the mean in global.gm.dat and I can use that value for sca

Re: [Freesurfer] License error on Windows Subsystem for Linux

Hi Lunhao, Interesting. Can you provide some details on the configurations where this worked? Were you using the same linux subsystem and windows versions? thanks Andrew From: on behalf of Shen Lunhao Reply-To: FS Help Date: Friday, November 20, 2020 at 2:44 AM To: FS Help Subject: [Freesu

Re: [Freesurfer] eddy_correct with DTI {Disarmed}

External Email - Use Caution Hi, Douglas Sorry to bother you again, do you think the problem is the old version of FSL? Best, Wei On Fri, Nov 13, 2020 at 1:32 PM Wei Shao wrote: > Hi Douglas > > I think it's 5.0.11 > > [weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesur