Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Priyanka Mehta]

Hi again

I want to use my hippocampal segmentation for masking 2380 brain volumes.
Is there a way to find out using Freesurfer if the hippocampal subfields
and the 2380 volumes are in the same space? The mean of the 2380 volumes
and the hippocampal subfields align correctly when I use Freesurfer's
freeview to view them. But does that also mean they are in the same voxel
space?

And if they aren't in the same space, is there any way using Freesurfer
that I can have the two in the same space?

I really appreciate any suggestions!

Thanks,
Priyanka Mehta

On Tue, Aug 25, 2015 at 4:50 PM, Bruce Fischl 
wrote:

> of course
> On Tue, 25 Aug 2015, Priyanka wrote:
>
> > Thanks Bruce. Just wanted to make sure I've got the correct output.
> >
> > Really appreciate the help.
> >
> > Thanks again,
> > Priyanka Mehta
> >
> >> On Aug 25, 2015, at 4:44 PM, Bruce Fischl 
> wrote:
> >>
> >> Hi Priyanka
> >>
> >> that is what mri_extract_label is designed to do. This facilitates
> making density maps in a common space. If you want to get the original
> label # back you can use something like:
> >>
> >> mri_binarize --match 128 --binval  or something like
> that
> >>
> >> cheers
> >> Bruce
> >>
> >>
> >>> On Tue, 25 Aug 2015, Priyanka Mehta wrote:
> >>>
> >>> Reposting my question:
> >>> This happens for all the segments that I've tried to extract using
> >>> mri_extract_label. They all show up as 128 nerve after
> mri_extract_label. Is
> >>> this a bug in the dev version?
> >>> Any help is greatly appreciated!
> >>> On Thu, Aug 20, 2015 at 3:45 PM, Priyanka  >
> >>> wrote:
> >>>  This happens for all the segments that I've tried to extract
> >>>  using mri_extract_label. They all show up as 128 nerve after
> >>>  mri_extract_label. Is this a bug in the dev version?
> >>>
> >>> > On Aug 20, 2015, at 3:20 PM, Lee Tirrell
> >>>   wrote:
> >>> >
> >>> > It seems that the command:
> >>> >
> >>> > mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
> >>> >
> >>> > put a value of 128 in lh.CA1.nii for the voxels labeled as 206
> >>>  in lh.hippoSfLabels-T1.v10.mgz. You can run:
> >>> >
> >>> > mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
> >>> >
> >>> > and then the correct label names from the Lookup Table will
> >>>  show up.
> >>> >
> >>> > Best,
> >>> > Lee
> >>> >
> >>> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote:
> >>> >>
> >>> >> Hi Eugenio
> >>> >> Thank you for the explanation, it makes sense to me now.
> >>> >> When I use Freeview to overlay my lh.CA1.nii on T1.nii, it
> >>>  aligns correctly. However, when I view the segmentation
> >>> >> with color map set to Lookup Table and 'show existing labels
> >>>  only' checked, the lh.CA1.nii segment shows as 128 Nerve
> >>> >> label. Shouldn't it still be showing up as 206 CA1 label? I
> >>>  am confused.
> >>> >>
> >>> >> On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias
> >>>   wrote:
> >>> >>  Hi Prya,
> >>> >>  that is because MriCron is not that great at overlaying
> >>>  images that are in the same physical space but not
> >>> >>  in the same voxel space. You have two options here:
> >>> >>  1. Use FreeSurfer's Freeview rather than MriCron to
> >>>  visualize the output. FreeView will correctly overlay
> >>> >>  the segmentation.
> >>> >>  2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
> >>>  lh.hippoSfLabels-T1.v10.mgz) when you call
> >>> >>  mri_extract_label. That volume lives in the same voxel
> >>>  space as T1.nii, and should be properly overlayed
> >>> >>  by MriCron. However, the resolution of the segmentation
> >>>  will be 1 mm, rather than the 0.333 mm that you'd
> >>> >>  get in option 1.
> >>> >>  Cheers,
> >>> >>  Eugenio
> >>> >>
> >>> >>  Juan Eugenio Iglesias
> >>> >>  Postdoctoral researcher BCBL
> >>> >>  www.jeiglesias.com
> >>> >>  www.bcbl.eu
> >>> >>
> >>> >>  Legal disclaimer/Aviso legal/Lege-oharra:
> >>>  www.bcbl.eu/legal-disclaimer
> >>> >>
> >>> >>  - Original Message -
> >>> >>  From: "Priyanka Mehta" 
> >>> >>  To: "Freesurfer support list"
> >>>  
> >>> >>  Sent: Wednesday, August 19, 2015 7:50:12 PM
> >>> >>  Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version
> >>>  Output
> >>> >>
> >>> >>  Hi
> >>> >>
> >>> >>  This is a follow-up question to my previous problem.
> >>> >>  After I run recon-all -all -i ${subject}.nii -subject
> >>>  ${subject} -hippocampal-subfields-T1, I extracted
> >>> >>  the left CA1 using mri_extract_label
> >>>  lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
> >>> >>  I used MRICro to overlay this lh.CA1.nii on my T1.nii,
> >>>  however the alignment is not correct (see atta

[Freesurfer] Questions about the correction methods in Surfstat

[chenhf_uestc]

Dear Surfstat Users,

I have a question about the RFT correction method in the 
Surfstat(http://www.math.mcgill.ca/keith/surfstat/).
In the online manual, the command to perform RFT correction is as follows:
[ pval, peak, clus ] = 
SurfStatP( slm, mask );


pval.P contains P-values for peaks, and pval.C contains P-values for clusters. 
This special structure is recognised by SurfStatView which draws the figure in 
a special way:

SurfStatView( pval, avsurf, 'Males-females removing age' ); 

The output figure is attached. In the colorbar of the figure, left represents 
cluster corrected p value and right one represents the vertex corrected p 
value, right? So, the warm color region in the figure can be survived by the 
RFT vertex correction, and the cool color region in the figure can be survived 
by the RFT cluster correction, right? If so, the regions with either warm or 
cool color region that can be survived after correction. When I report the 
results, I can report the regions with warm color (vertex level correction) or 
report the regions with cool color (cluster level correction), right?

In addtion, how can I understand the region overlapped by the warm and cool 
color (like he postier cingulate cortex), can simultaneously pass double 
correction of vertex level and cluster level? 

The final question is about the RFT cluster correction method, in the SPM or 
other software (like REST). Generally, on the cluster level correction, you 
should be based on a voxel (vertex) uncorrected height threshold of e.g. 
p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, 
right? What is the detailed correction procedure in the Surfstat software?

Any help would be greatly appreciate.

Best,
Feng___
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Re: [Freesurfer] White matter volume

[Bruce Fischl]

Hi John

I'm actually not sure how fslstats works. I'll cc MJ so he can answer that 
part of it. When we measure volume (e.g. in the stats files) we do partial 
volume correction as opposed to counting voxels, which we have found to be 
more accurate and repeatable.


cheers
Bruce

On Sat, 12 Sep 2015, John Anderson wrote:


Hi Bruce,
Kindly I want to inquire about the difference between white matter volume
generated by freesurfer ( specifically the white matter parcellations volume
mentioned in wmparc.stats) and the vwhite matter volume generated by other
tools like fslstats.
For example:
If I use a binarized mask from wmparc.mgz for the precentral gyrus in the
command : fslstats -i MPRAGE.nii.gz ( reoriented and skull stripped) -k
 -V 
Then
What is the differecne between this volume generated by "fslstats" and the
precenral gyrus volume mentioned in wmparc.stats. Which one is more
accurate?
 
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 4and the white matter volume generated by other methods
like using fslstats19 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.