Re: [Freesurfer] Percent Signal Change

That does not get computed. You can do it in matlab with something like

f = MRIread('f.nii.gz');

fmn = mean(f.vol,4);

fmnrep = repmat(fmn,[1 1 1 size(f.vol,3)]);;

s = f;

s.vol = f.vol./fmnrep;

MRIwrite(s,'percentchange.nii.gz')

On 02/15/2018 02:03 PM, Sarah Cole wrote:

Yes, that's exactly what I am looking for. Raw waveform as a percent.

On Thu, Feb 15, 2018 at 1:00 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

h-offset is the intensity offset (basically the mean signal). h.nii.gz
is a complicated combination of the betas (regression
coefficients) that
is included for backwards compatibility. What do you mean by % signal
change? Do you want the raw waveform as a percent?


On 02/15/2018 01:52 PM, Sarah Cole wrote:
> Thank you, Doug.
>
> Sorry for not being clear. Could you please tell me what
h.nii.gz and
> h-offset.nii.gz are?
>
> Also, do you have any recommendation on how to get % signal
change on
> the signal intensity as oppose to % signal change on contrasts?
>
> Thank you
>
> On Thu, Feb 15, 2018 at 12:47 PM, 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:
>
>     It divides the contast (ces) by voxel-wise mean. I'm not sure I
>     understand your quesstion about h and h-offset
>
>
>     On 02/15/2018 01:04 PM, Sarah Cole wrote:
>     > Hi,
>     >
>     > Could someone please let me know how to get the percent signal
>     change
>     > for raw signal intensity?
>     >
>     > I think the cespct.nii.gz gives me the contrast as %.
However, I am
>     > not sure about dividing h.nii and h-offset.nii. What are they?
>     >
>     >
>     > Thank you
>     >
>     >
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>     MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

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