Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

2016-09-17 Thread Ajay Kurani
Hi Anderson, Thanks for the help. When viewing my results they looked very strange. Upon further investigation it looks as though the mask I supplied to PALM was a white matter mask (mask.mgh from running qdec initially) created when I ran qdec. I assumed this would be the whole cortex but I w

[Freesurfer] Unpacking DWI Data

2016-09-17 Thread Emily Louise Belleau
Hello Freesurfer Experts, Our research team has recently collected data from Martinos Center. The entire scanning protocol (including anatomical, functional runs, DWI) is in one directory. Therefore I have been using unpacksdcmdir to tell me what runs go with each scanning sequence. I have h

[Freesurfer] Any binaries while Martinos disks being repaired / FTP server is down?

2016-09-17 Thread DT
I tried to download the current freesurfer release from the FTP site, and got a 550 error. After searching, I found the mailing list discussion of the disk problems / server outage with no ETA for its return. (here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046338.html and he

Re: [Freesurfer] area and smoothing

2016-09-17 Thread Seung Gul Kang
Hi Anderson, Thank you so much for your answer. I really appreciate it. All the Best, Seung-Gul ᐧ --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong

[Freesurfer] Longitudinal surface analysis of PET data

2016-09-17 Thread Matthieu Vanhoutte
Dear Freesurfer’s experts, I would like to use the longitudinal mixed-effects model for surface PET analysis. Although I could find all the process to follow the longitudinal analysis of cortical thickness, I couldn’t resolve the steps/commands to apply successively to coregistered PET data on

Re: [Freesurfer] area and smoothing

2016-09-17 Thread Anderson M. Winkler
Hi Seung-Gul, Please see below: On 16 September 2016 at 00:52, Seung Gul Kang wrote: > Dear Freesurfer experts, > > 1. I want to compare the area and/or areapial between two groups in qdec > menu. > I think that the eTIV or total surface area should be used as a covariate. > Which is more appro