Hi Da-Yea
you would need to compute the jacobian of the warping and apply it at
each voxel to scale the volumes (accounting for the warping).
cheers
Bruce
On Fri, 29 Mar
2019, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
I’m trying to extract regions (mri_e
External Email - Use Caution
Hello,
I'm trying to extract regions (mri_extract_label) of interest from the aseg.mgz
files and compare them to our manual segmentations. I've warped these ROI masks
onto our native space. I've noticed on the forum that there were mentions of
discr
External Email - Use Caution
It is a volume based study so I will continue to use mgx .25.
Thank you!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
On Mon, Fe
When you specify the --seg, just use gtmseg.mgz and not the whole path.
For mgx, I'd need to know what you intend to do with it. Is it a
surface-based study? If so, then I'd go with .01 in stead of .25
On 2/25/19 11:05 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
External Email - Use Caution
Hello,
I am currently trying to run PVC for my adc images using the following
script.
mri_gtmpvc --i
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc-masked.nii.gz
--reg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.lta
--psf
Hi Freesurfers,
We are trying to apply the PVC process to our PET images.
We proceeded through step3 as indicated on fswiki, and obtained the files:
- gtm.nii
- nopvc.nii
- mgx.gm.nii
How can we obtain the corrected uptake values from these files?
Can we obtain a corrected volume file for voxel bas
the binaries will be in the upcoming 6.0 and we could give you a beta
version pretty soon if you like. Rebecca (ccd) might have some
documentation that you can use, but I'm not sure.
cheers
Bruce
On Mon, 27 Apr 2015, K. Wagstyl
wrote:
> Hi Bruce,
>
> Thanks for this. I did see this paper and
Hi Bruce,
Thanks for this. I did see this paper and would like to try the
correction method - is it included in a new release of freesurfer or is
it a separate script?
If it's separate, would it be possible to try it?
Many thanks,
Konrad
On 2015-04-27 13:43, Bruce Fischl wrote:
> Hi Konrad
>
Hi Konrad
if you read Rebecca Shafee's recent paper:
http://www.ncbi.nlm.nih.gov/pubmed/25449739
you can see what we do about this kind of thing. The stream is largely
undocumented but you are welcome to try it out if you like.
cheers
Bruce
On Mon, 27 Apr 2015, K. Wagstyl wrote:
> Hi,
>
> I
Hi,
Is there a way to address or account the effects of partial voluming
when sampling grey matter intensity (mri_vol2surf)?
In particular, where there is cortical thinning, I'm also finding
intensity changes that could either be due to changes in the amount of
partial voluming or a change in
yes, it is
On Thu, 11 Jun 2009, Nasim Maleki wrote:
Dear Freesurfer developers,
I'm wondering whether the wmparc.stats is computed with a partial volume
correction at the boundaries of the structures.
Thank you,
Nasim
___
Freesurfer mailing lis
Dear Freesurfer developers,
I'm wondering whether the wmparc.stats is computed with a partial
volume correction at the boundaries of the structures.
Thank you,
Nasim
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.har
rmation as aseg.stats only provides the total volume for each label.
Thanks,
Anthony
--- On Thu, 5/3/09, Bruce Fischl wrote:
From: Bruce Fischl
Subject: Re: [Freesurfer] partial volume correction in mri_segstats
To: "Anthony"
Cc: freesurfer@nmr.mgh.harvard.edu
Date: Thursday, 5 March
wrote:
From: Bruce Fischl
Subject: Re: [Freesurfer] partial volume correction in mri_segstats
To: "Anthony"
Cc: freesurfer@nmr.mgh.harvard.edu
Date: Thursday, 5 March, 2009, 11:04 AM
Hi Anthony,
we're happy to provide the code, but there's no easy way to get a mask,
since e
class (e.g WM) after partial volume correction using FS ? Or is it
possible for you to provide more details of it so I can reproduce the
calculation to get the mask ?
Anthony
--- On Thu, 5/3/09, Bruce Fischl wrote:
From: Bruce Fischl
Subject: Re: [Freesurfer] partial volume correction in mr
Fischl wrote:
From: Bruce Fischl
Subject: Re: [Freesurfer] partial volume correction in mri_segstats
To: "Anthony"
Cc: freesurfer@nmr.mgh.harvard.edu
Date: Thursday, 5 March, 2009, 9:33 AM
Hi Anthony,
it should be more accurate (and more reliable in our studies). It
estimates
Hi Anthony,
it should be more accurate (and more reliable in our studies). It
estimates the volume fraction of each tissue class on the border of the
structure, assuming it is mixed with adjacent classes by estimating the
local mean of the two tissue classes, then computing the mixing
coeffic
Hi all,
In recon-all pipeline , mri_segstats runs with -pv mri/norm.mgz
option ,as written from
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats , it is used to
compensate partial voluming. I wonder what exactly does this do, as the volumes
given by aseg.stats are different from
aseg.mgz a
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