Hello Tom
Images look fine as they should be. But the main concern is regarding
the volume measurements which show higher volumes in gray matter as
compared to white matter. Shouldn't this be opposite?
Regards,
Divesh Thaploo
Junior Research Fellow (JRF)
Department of Neurosurgery
NIMHANS, Bangalore
+918952015510
On Tue, Jan 15, 2019 at 4:47 PM Tom Whyntie <[log in to unmask]> wrote:
>
> Hi Divesh,
>
> Great, thanks - all looks good!
>
> In which case, do the images you see with fsleyes for each of the pve_0, pve_1, pve_2 images look like what you'd expect for CSF, GM, and WM anatomically?
>
> Thanks, Tom
>
> ________________________________
> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Divesh Thaploo <[log in to unmask]>
> Sent: 15 January 2019 11:14:56
> To: [log in to unmask]
> Subject: Re: [FSL] FAST Segmentation
>
> I am attaching the screenshot of the FAST GUI.
> After FAST, pve_0, pve_1,pve_2.nii.gz files were created and others as
> well. I separately calculated the vol in mm3 using fslstats by taking
> mean and multiplying with the vol using the command you had mentioned
> in hyperlink.Do let me know if anything else is required.
>
> Regards,
> Divesh Thaploo
> Junior Research Fellow (JRF)
> Department of Neurosurgery
> NIMHANS, Bangalore
> +918952015510
>
> On Tue, Jan 15, 2019 at 4:34 PM Divesh Thaploo <[log in to unmask]> wrote:
> >
> > Hi Tom
> >
> > I am attaching the screenshot of the FAST GUI.
> > After FAST, pve_0, pve_1,pve_2.nii.gz files were created and others as well. I separately calculated the vol in mm3 using fslstats by taking mean and multiplying with the vol using the command you had mentioned in hyperlink.Do let me know if anything else is required.
> >
> > On Tue 15 Jan, 2019, 4:11 PM Tom Whyntie <[log in to unmask] wrote:
> >>
> >> Hi Divesh,
> >>
> >>
> >> Thanks for your email - could you let us know the options you used when running FAST please?
> >>
> >>
> >> You can double check your GM/WM estimates using the commands described in the FAST FAQ here:
> >>
> >>
> >> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST/FAQ
> >>
> >>
> >> (fslstats is your friend in this case.)
> >>
> >>
> >> The partial volume estimates for each tissue are in the *_pve_[0,1,2] output images (0=CSF, 1=GM, and 2=WM). If you could let us know some typical values we could investigate further.
> >>
> >>
> >> It may also be worth visually inspecting the PVE output images with fsleyes to see what FAST is doing.
> >>
> >>
> >> Thanks, Tom
> >>
> >> ________________________________
> >> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Divesh Thaploo <[log in to unmask]>
> >> Sent: 15 January 2019 05:47:11
> >> To: [log in to unmask]
> >> Subject: [FSL] FAST Segmentation
> >>
> >> I am running FAST Segmentation in cases of Brachial plexus injury as well as Controls, I have found Gray matter to be more than White matter. To my knowledge, it should be opposite. Can anyone explain?
> >>
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