[Freesurfer] Requesting passcode for freesurfer virtual machine

External Email - Use Caution Dear Free Surfer experts, I would like you to send the passcode to use this file: “FS_7_2_0_ubuntu_18_04_06.ova.7z. Regards. Minori Miyasaka === Name:宮坂実祈 Mail:u6505...@ecs.osaka-u.ac.jp

[Freesurfer] No flt available for tract training files

External Email - Use Caution Hello, I am trying to to run trac-all and I am getting the following error when using the FSL Flirt registration in the prior fitting step, due to the flt files not being available for the tract training subjects: WARN: Could not open

Re: [Freesurfer] Error in longitudinal process step 3

External Email - Use Caution Hi Lisa, The first line of 'base-tps' is causing the error - 'cp: cannot stat '/dfs8/pub/ltaylor2/downs/6008/mri/transforms/6008_6008_to_6008.lta': No such file or directory'. Did you pass 6008_6008 as one of the time points for recon-all base

Re: [Freesurfer] Error in longitudinal process step 3

External Email - Use Caution Hi Yujing, I've attached the base recon-all.log for review. Not sure which directory would be considered cross? There is a file name 'base-tps', and I am not sure why it populates a 6008_6008? [ltaylor2@login-i16:/pub/ltaylor2/downs/6008] $cat

Re: [Freesurfer] Error in longitudinal process step 3

External Email - Use Caution Hi Lisa, Can you show what your 'base-tps' in your base directory looks like? I think recon-all uses it to form the lta name (6008_6008_to_6008.lta). Can you also send your recon-all.log for base and cross maybe? Best, Yujing From:

Re: [Freesurfer] Error in longitudinal process step 3

External Email - Use Caution Hi Yujing, Yes, that is correct that 6008_tp1 is timepoint 1. Originally, I only had 6008_tp1,2 & 3, and when I ran step 2 the base was created. There were no errors when I ran step 2. Here's what's in the 6008/mri/transforms/ directory:

Re: [Freesurfer] Longitudinal SAMSEG with multi-contrast data

External Email - Use Caution Hi Gonzalo, Assuming that you have run mri_robust_template and obtained longitudinally registered images (e.g., tp0_t1_reg.mgz, tp1_t1_reg.mgz, etc...), then you can co-register each additional contrast of each time point with the commands:

[Freesurfer] Longitudinal SAMSEG with multi-contrast data

External Email - Use Caution Hi: How can I generate "tp1_flair_reg.mgz" image appeared in command "run_samseg_long --timepoint tp0_t1_reg.mgz tp0_flair_reg.mgz --timepoint tp1_t1_reg.mgz tp1_flair_reg.mgz --timepoint tp2_t1_reg.mgz tp2_flair_reg.mgz --output outputDir/" ?

[Freesurfer] VM password

External Email - Use Caution Hello. I would like the password to the Ubuntu VM that has Freesurger installed on it. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Generate Stats File for fornix.mgz in T1 weighted MRI ?

External Email - Use Caution Hi Ahsan, Can you try mri_segstats?

Re: [Freesurfer] Error in longitudinal process step 3

External Email - Use Caution There should be a file named 'base-tps' in your base directory. it should contain all the -tp <> passed to your base processing, and they should agree with to your cross and long processing. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf

Re: [Freesurfer] Error in longitudinal process step 3

External Email - Use Caution Hi Lisa, I'm wondering what your naming convention is. Here is tutorial page for longitudinal processing:

[Freesurfer] trac-all ERROR: Option syn/acomm.flt.prep.trk unknown

External Email - Use Caution Hello, I am attempting to run white matter tractography using TRACULA, as described in the tutorial, however, using a brain parcellation acquired using an external algorithm. I have put the aparc+aseg.mgz file in the subject directory in folder mri