The data in gtm.nii.gz is in floating point. If you want to change the
gtm.stats file, you'll have to rescale the input, eg, fscalc
input.nii.gz mul 1000 -o input-time-1000.nii.gz
On 08/15/2017 04:09 AM, Shane Schofield wrote:
> Hello Dr Greve,
>
> I have ran the command and got the data from t
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 trie
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
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 a
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
wrote:
Hello Dr Greve,
I hav
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
wrote:
You will need to run gtmseg --s su
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 --re
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
Hi Dr Greve,
Thank you very much! I will use the MGX CTX volume for the surface sampling.
Best Wishes,Shane.
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve
wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the
PETsurfer page. Run it with --psf 0 and use
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
> m
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
t: Re: [Freesurfer] Mean diffusivity on cortex?
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, Ye
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
wrote:
Agreed, especially so with MD. K
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, "
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
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
re
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
O
@yahoo.com]
Sent: Friday, August 11, 2017 6:42 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Mean diffusivity on cortex?
Hi Dr Yendiki, I am studying a group of people with APOE4 and I want to see
whether cortical MD increases can be detected relative to non-carriers, and if
so, is
Hi Dr Yendiki, I am studying a group of people with APOE4 and I want to see
whether cortical MD increases can be detected relative to non-carriers, and if
so, is the effect size bigger than changes in cortical thickness.
On Friday, August 11, 2017, 11:19:32 AM GMT+1, Yendiki, Anastasia
wrote:
What effect are you trying to measure with MD on the cortex?
From: Shane Schofield [shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 3:12 AM
To: Freesurfer Support List; Yendiki, Anastasia
Subject: Re: Mean diffusivity on cortex?
Thanks Dr Yendiki.
I am m
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 t
/AnatomicalROIV6.0
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Shane Schofield
[shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 2:03 AM
To: Freesurfer Support List
Subject: [Freesurfer] Mean diffusivity on cortex
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.
__
Cool !
Thanks
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, July 01, 2014 3:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mean diffusivity (MD)
The mean
The mean diffusivity is the same as the apparent diffusion coef (ADC);
there should be an adc volume in the output of dt_recon
doug
On 07/01/2014 12:38 PM, Alshikho, Mohamad J. wrote:
> Thanks Doug,
> Actually I want to calculate the MD just for the right and left hemispheric
> white matter.
>
Thanks Doug,
Actually I want to calculate the MD just for the right and left hemispheric
white matter.
The output of dt_recon doesn't include anything about the mean diffusivity (i.e
we have just the eignvals.nii ) so what is the best way to generate the MD as a
nifty file? Is it by using fslspl
Sorry, I have no idea what is reasonable (I don't do a lot of DTI
analysis myself). The variability in the CC is worrisome. Maybe someone
else can chime in
doug
On 03/25/2014 06:16 AM, Rotem Saar wrote:
> Hi Doug,
>
> Thanks for your help.
> I got the attached output for the MD calculation - do
Hello all,
I have run bedpostx on a series of DTI scans over ~1 year, the earlier
ones in stable 5.1 and latter. I'm seeing quite a lot of variability in
intensity from the earlier to later versions -
re-running bedpostx in 5.3 on an older scan and comparing with 5.1 yields
up to 10% variation
NAME/DTI/fa-masked.mgz --sum
> /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa-masked
what went wrong? You can add --seg-erode 1 to this cmd line (if you have
5.3)
>
>
> Message: 26
> Date: Tue, 04 Feb 2014 11:10:25 -0500
> From: Douglas N Greve <mailto:
.mgz --sum
/usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa-masked
Message: 26
Date: Tue, 04 Feb 2014 11:10:25 -0500
From: Douglas N Greve
Subject: Re: [Freesurfer] Mean diffusivity
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <52f110f1.5050...@nmr.mgh.harvard.edu>
Content-Type
Use mri_label2vol to transfer the wmparc.mgz into the DTI space, then
use mri_segstats with --seg-erode 1 to compute summaries of the MD in
each region
doug
On 02/03/2014 10:45 PM, Rotem Saar wrote:
> Dear freesurfer experts,
>
> Can u please advise on how to extract the mean diffusivity value
Dear freesurfer experts,
Can u please advise on how to extract the mean diffusivity value for each
ROI from the wmparc file ?
I know how to extract the FA value, but interested in the MD value also for
the same regions.
Thanks
Rotem
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
B
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