Re: [Freesurfer] Percent Signal Change

[Douglas N. Greve]

fmn is the mean image averaging over all time points, so it should have 
the same dimensions as one of your images. The repmat() call is supposed 
to replicate the image over the number of time points, but there is a 
bug. It should be f.vol,4 not 3. Try that


On 04/03/2018 02:33 PM, Sarah Cole wrote:
> Doug,
>
> Could you please let me know what this line is doing?
> "fmnrep = repmat(fmn,[1 1 1 size(f.vol,3)]);"
>
> When I try to assign f.vol/fmnrep to s.vol (this line s.vol = 
> f.vol./fmnrep;), matrices do not match in dimension.
>
> Thanks,
> S
>
> On Thu, Feb 15, 2018 at 1:05 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> 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
> > mailto:gr...@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
> >     >  
> >
> >      
> >       >     >
> >     >     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
> >     >     >
> >     >     >
> >     >     > ___
> >     >     > Freesurfer mailing list
> >     >     > Freesurfer@nmr.mgh.harvard.edu
> 
> >      >
> >     >      
> >      >>
> >     >     >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> >   
>   >
> >     >   
>   
> >   
>   >>
> >     >
> >     >     --
> >     >     Douglas N. Greve, Ph.D.
> >     >     MGH-NMR Center
> >     > gr...@nmr.mgh.harvard.edu
> 
> >
> >      
> >>
> >     >     Phone Number: 617-724-2358 
> >     >
> >     >     Fax: 617-726-7422   >    >
> >     >
> >     >     Bugs: surfer.nmr.mgh.harvard.edu/fs

Re: [Freesurfer] Percent Signal Change

[Sarah Cole]

Doug,

Could you please let me know what this line is doing?
"fmnrep = repmat(fmn,[1 1 1 size(f.vol,3)]);"

When I try to assign f.vol/fmnrep to s.vol (this line s.vol =
f.vol./fmnrep;), matrices do not match in dimension.

Thanks,
S

On Thu, Feb 15, 2018 at 1:05 PM, Douglas N Greve 
wrote:

> 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
> > mailto:gr...@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
> > > mailto:gr...@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
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > >
> > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > >  > >
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu 
> >  >>
> > > Phone Number: 617-724-2358 
> > >
> > > Fax: 617-726-7422   > >
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > >  > >
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > >  > >
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > >  > >
> > > Outgoing:
> > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> > >  flat/greve/
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> >  > >
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > >
> >   > 

Re: [Freesurfer] Percent Signal Change

[Douglas N Greve]

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 
> mailto:gr...@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
> > mailto:gr...@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
> >     >
> >     >
> >     > ___
> >     > Freesurfer mailing list
> >     > Freesurfer@nmr.mgh.harvard.edu
> 
> >      >
> >     >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> >      >
> >
> >     --
> >     Douglas N. Greve, Ph.D.
> >     MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> >
> >     Phone Number: 617-724-2358 
> >
> >     Fax: 617-726-7422   >
> >
> >     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> >      >
> >     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> >      >
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> >      >
> >     Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> >      >
> >
> >     ___
> >     Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> >   
>   >
> >
> >
> >     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
> 
> >        

Re: [Freesurfer] Percent Signal Change

[Sarah Cole]

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 
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
> > mailto:gr...@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
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> >
> > 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.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Percent Signal Change

[Douglas N Greve]

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 
> mailto:gr...@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
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> 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.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Percent Signal Change

[Sarah Cole]

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  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
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Percent Signal Change

[Douglas N Greve]

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
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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[Freesurfer] Percent Signal Change

[Sarah Cole]

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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Re: [Freesurfer] percent signal change

[Douglas N Greve]

I think you'll need to contact the FSL list to ask how to convert the 
COPE volume to a voxel-wise percent signal change. Once you have that, 
then you can just project that data onto the surface instead of the 
original COPE.
doug


On 07/24/2015 05:11 PM, Mariam Sood wrote:
> Dear Doug,
>
> Thank you for the reply. I want to use the percent change in signal as a 
> measure of effect size for various regions of interest, so would ideally like 
> an average percent signal change in that ROI. I want it at the group data 
> though. Much appreciate your suggestions.
>
> Many thanks,
> Mariam.
>
>
> On 24 Jul 2015, at 17:37, Douglas Greve  wrote:
>
>> what kind of percent output do you want? FSL does a global
>> normalization, effectively computing percent change (actually 10th of
>> percent change I think). If you want voxel-wise percent, then it is more
>> difficult.
>>
>> On 7/24/15 11:11 AM, Mariam Sood wrote:
>>> Dear Doug,
>>>
>>> I am using the FSL-Freesurfer pipeline, with single subject analysis done 
>>> in Feat and group analysis done using mri_glmfit. Is there a way I can 
>>> calculate percent signal change from the group analysis output (or any 
>>> other method which combines single subject output)?
>>>
>>> Many thanks,
>>> Mariam.
>>>
>>>
>>> Mariam Sood
>>> PhD student
>>> Department of Psychological Sciences
>>> Birkbeck, University of London
>>>
>>>
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>>>
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>> dispose of the e-mail.
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Re: [Freesurfer] percent signal change

[Mariam Sood]

Dear Doug,

Thank you for the reply. I want to use the percent change in signal as a 
measure of effect size for various regions of interest, so would ideally like 
an average percent signal change in that ROI. I want it at the group data 
though. Much appreciate your suggestions. 

Many thanks,
Mariam. 


On 24 Jul 2015, at 17:37, Douglas Greve  wrote:

> what kind of percent output do you want? FSL does a global 
> normalization, effectively computing percent change (actually 10th of 
> percent change I think). If you want voxel-wise percent, then it is more 
> difficult.
> 
> On 7/24/15 11:11 AM, Mariam Sood wrote:
>> Dear Doug,
>> 
>> I am using the FSL-Freesurfer pipeline, with single subject analysis done in 
>> Feat and group analysis done using mri_glmfit. Is there a way I can 
>> calculate percent signal change from the group analysis output (or any other 
>> method which combines single subject output)?
>> 
>> Many thanks,
>> Mariam.
>> 
>> 
>> Mariam Sood
>> PhD student
>> Department of Psychological Sciences
>> Birkbeck, University of London
>> 
>> 
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>> 
> 
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Re: [Freesurfer] percent signal change

[Douglas Greve]

what kind of percent output do you want? FSL does a global 
normalization, effectively computing percent change (actually 10th of 
percent change I think). If you want voxel-wise percent, then it is more 
difficult.

On 7/24/15 11:11 AM, Mariam Sood wrote:
> Dear Doug,
>
> I am using the FSL-Freesurfer pipeline, with single subject analysis done in 
> Feat and group analysis done using mri_glmfit. Is there a way I can calculate 
> percent signal change from the group analysis output (or any other method 
> which combines single subject output)?
>
> Many thanks,
> Mariam.
>
>
> Mariam Sood
> PhD student
> Department of Psychological Sciences
> Birkbeck, University of London
>
>
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>

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[Freesurfer] percent signal change

[Mariam Sood]

Dear Doug,

I am using the FSL-Freesurfer pipeline, with single subject analysis done in 
Feat and group analysis done using mri_glmfit. Is there a way I can calculate 
percent signal change from the group analysis output (or any other method which 
combines single subject output)? 

Many thanks,
Mariam. 


Mariam Sood
PhD student
Department of Psychological Sciences
Birkbeck, University of London


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Re: [Freesurfer] Percent signal change after resampling and combining FEAT analyses

[Douglas N Greve]

percent relative to what? FEAT will automatically rescale  to 1 (or 
something like that)
doug

On 03/25/2014 05:51 PM, Manuel Spitschan wrote:
> Dear FreeSurfer experts,
>
> I've performed a few first-level analyses of BOLD data with FSL, and have 
> followed the instructions on the FS Wiki 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat) to sample 
> the COPEs of each run to a common surface (fsaverage) and run a fixed-effects 
> analyses using 'mri_glmfit' across the runs.
>
> The resulting gamma.mgh contains the COPEs per vertex across the runs. How 
> would I find out the appropriate scaling factor and the baseline image to 
> calculate percent signal change per vertex following these analysis steps?
>
> Any help would be appreciated.
>
> Thanks in advance,
>
> Manuel Spitschan
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] Percent signal change after resampling and combining FEAT analyses

[Manuel Spitschan]

Dear FreeSurfer experts,

I've performed a few first-level analyses of BOLD data with FSL, and have 
followed the instructions on the FS Wiki 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat) to sample 
the COPEs of each run to a common surface (fsaverage) and run a fixed-effects 
analyses using 'mri_glmfit' across the runs.

The resulting gamma.mgh contains the COPEs per vertex across the runs. How 
would I find out the appropriate scaling factor and the baseline image to 
calculate percent signal change per vertex following these analysis steps?

Any help would be appreciated.

Thanks in advance,

Manuel Spitschan
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Re: [Freesurfer] percent signal change

[Doug Greve]

No, sorry, the raw timecourse would have to be analyzed.

Elif SIKOGLU wrote:


Hello.

I obtained the percent signal change using roisummary-sess. (divided 
the BOLD amplitude by the mean functional baseline offset to get the 
percent signal change.) Is there a way to get an error estimate (i.e. 
standard deivation) on this value? 


Thanks
Elif



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[Freesurfer] percent signal change

[Elif SIKOGLU]

Hello.
I obtained the percent signal change using roisummary-sess. (divided the
BOLD amplitude by the mean functional baseline offset to get the percent
signal change.) Is there a way to get an error estimate (i.e. standard
deivation) on this value?

Thanks
Elif
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Re: [Freesurfer] percent signal change

[Doug Greve]

Yes, it is. The h.nii file has a somewhat tortured format. If you just 
want the contrast as a percent, then look in the contast directory for 
cespct.


Elif SIKOGLU wrote:


Hello,


We want to get the percent signal change for the activated regions and 
for that we want to use the h.nii and h-offset.nii files.


We plan to divide the h.nii by h-offset.nii .


First of all is this a correct approach?


Second, h.nii has 4 frames in it, which one do we really need?


Thanks

Elif



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[Freesurfer] percent signal change

[Elif SIKOGLU]

Hello,


We want to get the percent signal change for the activated regions and for
that we want to use the h.nii and h-offset.nii files.

We plan to divide the h.nii by h-offset.nii .


First of all is this a correct approach?


Second, h.nii has 4 frames in it, which one do we really need?


Thanks

Elif
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[Freesurfer] Percent signal change: what stats to read

[raij]

Hi,

We have calculated a FIR group analysis with FS-FAST and have the
corresponding ces, cesvar, f, fsig, iminsig, minsig, sig, and t maps in
the contrast folders.

Which one of these should I use for presenting % signal change? We want to
do some further analyses of the group analysis results with matlab and
would need to use % signal change as the input values for those analyses.

Thanks,

Tommi

---
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
Bldg 149, 13th St
Charlestown, MA 02129
U.S.A.


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Re: [Freesurfer] Percent Signal Change

[Matt Cain]

Thanks for the suggestions. I'm trying to read in the h-offset volumes, 
but I can't figure out the correct matlab script to use. To read in the 
h volumes I'm using fast_ldsxabfile, but that assumes there is a file 
.dat and there's no h-rh-offset.dat. I could probably hack 
something together, but this sounds like a problem that's probably ben 
solved before...

-Matt
On Jun 16, 2004, at 16:14, Nick Knouf wrote:
What I do in "froi" is take the value at the particular voxel and 
divide by the h-offset value for that voxel and multiply by 100.  For 
ROIs, that's done individually for each voxel, and then averaged to 
get the value for the ROI.

To get the standard deviation is similar, except of course you can't 
simply average standard deviations, but rather I compute the variance 
for each voxel, average the variances together, and then compute the 
standard deviation.

The standard error is more complicated but I can give you more info if 
you'd like.

nick
On Jun 16, 2004, at 3:24 PM, Matt Cain wrote:
Greetings,
I'm trying to write a script to generate hemodynamic timecourses for 
particular voxels. I want to imitate the feature in tkmedit where 
these graphs can be viewed as Percent Signal Change.

I know how to generate this for averages across an ROI, but that 
involves computing the Average Baseline Activity,  a quantity which 
is tied to the size ROI and thus does not make sense to use for a 
single voxel.

Does anyone know what value is used to properly scale the hemodynamic 
timecourses and how to compute that value?

Thanks
Matt Cain
[EMAIL PROTECTED]
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Re: [Freesurfer] Percent Signal Change

[Nick Knouf]

What I do in "froi" is take the value at the particular voxel and 
divide by the h-offset value for that voxel and multiply by 100.  For 
ROIs, that's done individually for each voxel, and then averaged to get 
the value for the ROI.

To get the standard deviation is similar, except of course you can't 
simply average standard deviations, but rather I compute the variance 
for each voxel, average the variances together, and then compute the 
standard deviation.

The standard error is more complicated but I can give you more info if 
you'd like.

nick
On Jun 16, 2004, at 3:24 PM, Matt Cain wrote:
Greetings,
I'm trying to write a script to generate hemodynamic timecourses for 
particular voxels. I want to imitate the feature in tkmedit where 
these graphs can be viewed as Percent Signal Change.

I know how to generate this for averages across an ROI, but that 
involves computing the Average Baseline Activity,  a quantity which is 
tied to the size ROI and thus does not make sense to use for a single 
voxel.

Does anyone know what value is used to properly scale the hemodynamic 
timecourses and how to compute that value?

Thanks
Matt Cain
[EMAIL PROTECTED]
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[Freesurfer] Percent Signal Change

[Matt Cain]

Greetings,
I'm trying to write a script to generate hemodynamic timecourses for 
particular voxels. I want to imitate the feature in tkmedit where these 
graphs can be viewed as Percent Signal Change.

I know how to generate this for averages across an ROI, but that 
involves computing the Average Baseline Activity,  a quantity which is 
tied to the size ROI and thus does not make sense to use for a single 
voxel.

Does anyone know what value is used to properly scale the hemodynamic 
timecourses and how to compute that value?

Thanks
Matt Cain
[EMAIL PROTECTED]
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