[Freesurfer] Longitudinal data from different sequences and scanners

All, Our lab is working with longitudinal (two time points) data from a cohort of around 130 individuals. We are attempting to make comparisons between time points 1 and 2 on measures like total brain volume, ventricular volume, ventricle-brain-ratio, and cortical thickness. However, we have run

Re: [Freesurfer] Longitudinal data from different sequences and scanners

All, Just wanted to follow up on this message. Does anyone have recommendations for the best way to compare this data longitudinally? Thanks very much, James On Thu, Mar 29, 2018 at 1:19 PM, James Gullickson wrote: > All, > > Our lab is working with longitudinal (two time points) da

Re: [Freesurfer] Longitudinal data from different sequences and scanners

External Email - Use Caution Martin, Thanks for the feedback. Given our data set (1mm^3 timepoint1 and 0.8mm^3 timepoint 2), what would be the best way to salvage this data and look for longitudinal changes? Would it be possible to upsample/downsample the images so that they are t

[Freesurfer] Visualizing Supratentorial volume

External Email - Use Caution All, Is there any way to graphically visualize the segmentations for SupraTentorialVol and SupraTentorialVolNotVent, for example in freeview or tkmedit? Based on the descriptions I have read for the supratentorial values, I want to use them for an anal

Re: [Freesurfer] Visualizing Supratentorial volume

aseg. > Or do you want all the non-STV removed? If that, you can create a mask > of STV using mri_binarize and --match run on the aseg.mgz, then use > mri_mask aseg.mgz stvmask.mgz aseg-stvonly.mgz > > > > On 05/30/2018 11:56 AM, James Gullickson wrote: > > > > > &g

Re: [Freesurfer] Visualizing Supratentorial volume

mbers and use > mri_binarize with the --match option > > On 5/31/18 3:27 PM, James Gullickson wrote: > > External Email - Use Caution > Sorry I wasn't clear. Yes, I would like to see it with all the non-STV > removed, in order to see exactly what the supratentorial seg

[Freesurfer] Using grad_unwarp

External Email - Use Caution All, I am interested in using grad_unwarp. I have been reading up on the documentation a bit and from what I understand not all the necessary files are distributed with the public version of Freesurfer, due to proprietary information in the tables. How

[Freesurfer] Cortical Thickness at Individual Vertices

External Email - Use Caution All, I am comparing cortical thickness between subjects with and without mild traumatic brain injury (mTBI). So far the contrasts in QDEC have not been significant after correcting for multiple comparisons. I am not necessarily surprised at this due to

Re: [Freesurfer] Cortical Thickness at Individual Vertices (fwd)

that compare the whole distribution of > thicknesses across subject populations. You could do a t-test or > something > non-parametric like a Kolmogorov-Smirnov or use permutation testing. > I'll > cc Tom Nichols so he can chime in with something more s

[Freesurfer] Resample data for longitudinal comparisons

External Email - Use Caution All, I would like to compare cortical thickness between two timepoints. Timepoint 1 has 1mm^3 data. Timepoint 2 has 0.8mm^3 data. I realize that there are limitations with this change in resolution between timepoints and that no analysis is going to