[Freesurfer] Functional Connectivity Motion Regression

Hi Freesurfer list, My group is switching to the fsfast functional connectivity pipeline. We would like to continue regressing out the six-parameter rigid body head motion as a nuisance variable. In order to do this, which file should we flag: is it fmcpr.mcdat or mcprextreg? Thank you!

Re: [Freesurfer] mri_coreg

Actually, it is on by default (thanks to Emma for pointing it out). The smoothing helps to blur anatomical differences which reduces the chance that it will get stuck in a local minimum. It will usually only smooth the reference, and only if it is high res; this can help the reference look a

[Freesurfer] Using Total Cortical White Matter Volume as a "whole brain" covariate

Dear FreeSurfer Developers, I am using FreeSurfer 5.3 to analyze whether a risk factor explains variation in brain structures related to surface area, mean thickness, and subcortical volumes. Documentation suggests using estimated Total Intracranial Volume (eTIV) as a covariate to adjust

Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6)

We'll try to process it on a blade server tongiht... if it succeeds we can edit any incorrect results as needed. The image is from a separate site, it has OK resolution (1x1x1.5) but has an enormous amount of gibbs ringing compared to our on-site images, which is probably causing the issue...

Re: [Freesurfer] Continuous co-variate by continuous co-variate interaction effects

Is that your design matrix or the contrast matrix? To test for the interaction between two continuous variables, one usually creates a new variable by multiplying them together and then just testing for the regressor for that variable being different than zero On 08/23/2017 12:34 PM, Timothy

Re: [Freesurfer] recon-all error

does this happen every time you run it? The message said that the job was killed, which suggests something outside of recon-all (eg, if you were running it on a cluster, sometimes a job will get killed if it runs out of memory or runs too long). On 08/23/2017 02:30 PM, Cara Bohon wrote: > I

Re: [Freesurfer] Longitudinal stream for cross-sectional analysis?

Hi K, I would recommend to use the data from the longitudinal directories also for the cross sectional analysis. That data will be less noisy than from independent processing (which is what you also find). Since the longitudinal stream goes through many different processing steps than the

Re: [Freesurfer] Longitudinal freesurfer

Hi, healthy controls usually show 0.5% atrophy per year or less. You have very young subjects, and the expectation there would be near to 0 change. Due to acquisition noise, hydration effects, head motion etc, you will of course always find individual cases with volume / thickness increase

Re: [Freesurfer] Longitudinal spatiotemporal LME vs. V-LME

Hi Ann-Kathrin, for age you should use age at baseline (should be fixed for all time points per subject). You have the time_from_baseline variable to model the time. (maybe that is what you are already doing). I don't know why more survives with the voxelwise model, I usually see the

Re: [Freesurfer] longitudinal generic-time and spc

Hi Kasper, 1) yes correct 2) for generic the time delta is always 1 ( 2-1, 3-2, 4-3 ..) Best, Martin Am 16.08.2017 um 08:22 schrieb Kasper Jessen: Dear Freesurfer, The following is a follow-up, on a previous discussion

[Freesurfer] Continuous co-variate by continuous co-variate interaction effects

Freesurfer experts, I have created a design matrix in order to test for whether there is an interaction effect between two continuous co-variates controlling for a categorical variable. So I have one categorical variable with two levels, and two continuous co-variates. My design matrix is as

Re: [Freesurfer] Error after manual edits in freesurfer 6

Hi Chethana are you sure it is a problem with the volume? It may just be a visualization issue. Try changing the window levels cheers Bruce On Wed, 23 Aug 2017, Chethana wrote: > To, > The Freesurfer experts, > > I am analysing a set of MRI images in freesurfer 6. In the step 1 of >

Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6)

That defect is so big you probably ran out of memory. > On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D. > wrote: > > We encountered a hard failure, below is the tail of the log. We are currently > running Freesurfer 6 again locally to see if it succeeds on a

Re: [Freesurfer] QA tools for FS vs 6.0

Dear Antonietta, I don’t know of any official statement in that regard, however, Yong Li (CC’ed) seems to have updated the QA tools working with FS 6 in April. He may share his code. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im

[Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6)

We encountered a hard failure, below is the tail of the log. We are currently running Freesurfer 6 again locally to see if it succeeds on a desktop machine (this is the first time encountering a hard failure on the XNAT server). Any suggestions? -merging segment 180 into 178 160 defects

[Freesurfer] QA tools for FS vs 6.0

Dear FreeSurfer list, is any of you aware of a new version of the QA (quality assessment) tools < [ https://surfer.nmr.mgh.harvard.edu/fswiki/QATools | https://surfer.nmr.mgh.harvard.edu/fswiki/QATools ] > working for FS vs 6.0? Should I expect a new release in the near feature? Kind regards,

Re: [Freesurfer] hippocampal and amygdalar subregional segmentation

Hi Moji: 1. Absolutely. You can use standard FreeSurfer tools for extracting masks from a segmentation, resample them to whatever space, etc. 2. A lot of people have been making this question, so we’re now writing a bunch of merged segmentations to the mri directory of the subjects for

[Freesurfer] hippocampal and amygdalar subregional segmentation

Dear Freesurfer Developers, I have some questions regarding hippocampal and amygdalar subregional segmentation in the latest Freesurfer version: 1) Can one use the segmentation outputs as ROI masks, register those to native space functional image, and extract functional time courses in order