Hello Dr Greve, I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision? Thank you.
On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a
silly
idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu> wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD
varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
wrote:
Hi Shane
you probably don't need cvs as it is more to extend the
surface-based
registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me
to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
<shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>
wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface
like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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