Sorry, I don't know if that info is in PET dicom files
On 08/16/2017 07:14 PM, Shane Schofield wrote:
Okay I understand.
So I ideally would like to do the PetSurfer before actually working on the BPND but I already got them in the BPND format as well as the raw dynamic images. I tried to obtain the BPND data out from PetSurfer myself, but then I realise I don't any time.dat with me. mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat*time.dat* --o mrtm1 --no-est-fwhm --nii.gz Is there a way to extract the time.dat in the DICOM? Can you show me an example of what it is the correct time.dat so I can ask my colleagues if they have it somewhere?
Thanks a lot!!
On Wednesday, August 16, 2017, 10:46:09 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
SUVR you can. BP is a little trickier because BP estimation is a nonlinear operation that can be biased by noise. Probably it comes out similarly.
On 08/16/2017 02:50 PM, Shane Schofield wrote:
Hi Dr Greve,
On a similar note, can I use the Petsurfer on PET data that have already been averaged into a single frame 3D volume instead of 4D? Example, SUVR and BPND data.
Thanks for your help again.
On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield <shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com> wrote:
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 mailto: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 mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto: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
<mailto:AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu>
<mailto:AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu
<mailto: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
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu
<mailto: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
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu
<mailto: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 <mailto:shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>
<mailto:shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com
<mailto: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. > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
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