[Freesurfer] Longitudinal pipeline question

2020-07-28 Thread Rachel Romeo
External Email - Use Caution Hi, I am working with some longitudinal data that was originally run through troubleshooting/recon-all in freesurfer 5.3. A lot of time went into the edits, so I definitely do not want to replicate these in freesurfer 6. Do I need to run the

[Freesurfer] longitudinal spc over an ROI

2016-09-16 Thread Rachel Romeo
Hi, I have 3 participant groups in my data set, all with 2 longitudinal time points approximately evenly spaced. I've run everyone through the longitudinal pipeline, and used the Monte Carlo simulation to find a cluster that differs in SPC between groups 1 and 2. Now I want to calculate the

[Freesurfer] Some volumes not loading (corrupted?)

2016-09-13 Thread Rachel Romeo
Hi all, After doing some manual edits to the wm and pial masks, I recently had a recon fail with the following error: mghRead(/subject_177/mri/brainmask.mgz, -1): read error Invalid argument mri_em_register: could not open mask volume brainmask.mgz. When trying to load either the