Hello SPMers, in my experience the dark spots in the basal area in the temporal lobe means loss of signal because the suceptibility effects. The BOLD effect  is around the 5% of change of signal in 3T, it cannot explain the total loss of signal, please correct me if I am wrong.

John Ochoa

On Sat, Mar 12, 2011 at 9:26 AM, Vladimir Bogdanov <[log in to unmask]> wrote:

Dear Roberto Viviani,

Thank you for your reply.

Though, I did not understand the last sentence. "It adds to eny
> exeisting inhomegenity; if this latter has led to signal
> loss, you'll have little from which get the BOLD signal."

I have no deep knowledge of the physics of the processes. I am interested if the "dark spots" mean the loss or decrease of BOLD responses? Or, alternatively, the BOLD response is independent of the baseline level of the signal. It can be just additive. In this case and the only difference between "dark" and "normal" areas is in the "baseline" of the signal.

Please correct me if my logic is wrong.

Sincerely yours,
Vladimir

--- On Sat, 3/12/11, [log in to unmask] <[log in to unmask]> wrote:

> From: [log in to unmask] <[log in to unmask]>
> Subject: Re: [SPM] Explicit masking to improve signal in the OFC?
> To: "Vladimir Bogdanov" <[log in to unmask]>
> Date: Saturday, March 12, 2011, 2:18 PM
> Dear Vladimir,
>
> the loss of signal has to do with the physics of the
> generation of the MR signal. The effect of magnetic
> inhomogeneity on the signal is the following:
>
> -- there is loss of signal (less with shorter TE's)
> -- there is displacement of signal (irrespective of TE's)
>
> In typical T1-weighted structural images (typical in the
> sense of being obtained with gradient recall, like EPIs),
> these problems are less marked because the voxels are
> smaller, and hence less homogeneous.
>
> The BOLD signal is itself the effect of voxel
> inhomogeneity, modulated by oxygen content in blood, through
> its effects on the Fe in the heme group. It adds to eny
> exeisting inhomegenity; if this latter has led to signal
> loss, you'll have little from which get the BOLD signal.
>
> Best
> Roberto Viviani
>
>
> Quoting Vladimir Bogdanov <[log in to unmask]>:
>
> > Dear Roberto Viviani,
> >
> > This is often the case in our studies. We indeed use
> 3T scanner.  There are a lot of visible "black holes"
> in EPI images (see the  picture). In some subjects it
> is more pronounced, in others - less.
> >
> > What does it mean? There should be no task-related
> BOLD signal  responses from those areas? How to treat
> those inhomogeneities?
> >
> > Thank you in advance for your opinion!
> >
> > Sincerely yours,
> > Vladimir
> >
> >
> > --- On Sat, 3/12/11, Roberto Viviani <[log in to unmask]>
> wrote:
> >
> >> From: Roberto Viviani <[log in to unmask]>
> >> Subject: Re: [SPM] Explicit masking to improve
> signal in the OFC?
> >> To: [log in to unmask]
> >> Date: Saturday, March 12, 2011, 1:12 PM

> >> Dear Deborah,
> >>
> >> before concluding that signal in the OFC is being
> cut off,
> >> I'd check that this is indeed the case by
> overlaying the spm
> >> image over the mean EPI image as a template.
> Magnetic field
> >> inhomogenity in that region results in the brain
> shape in
> >> the EPI images to differ from that of the T1
> template brains
> >> used in displays, sometimes substantially. You
> might
> >> discover that you have no brain where you think
> the OFC is.
> >> This may be especially the case if you are using a
> 3T
> >> scanner.
> >>
> >> To mask your analysis, choose 'explicit masking'
> from the
> >> menu, after having prepared a 1/0 mask image for
> selection.
> >>
> >> Best,
> >> Roberto Viviani
> >>
> >> Quoting Deborah Tang <[log in to unmask]>:
> >>
> >> > Dear SPM Community,
> >> >
> >> > While analyzing results from a recent fMRI
> study, I
> >> have discovered
> >> > that I have very little activation in the
> lower
> >> regions of the brain. I
> >> > am concerned that SPM may have truncated my
> data in
> >> the lower regions
> >> > of the brain because they were below
> threshold. Since
> >> I am particularly
> >> > interested in activation in the OFC, this is
> a
> >> problem. Upon reviewing
> >> > my data (ie. mask.img), it looks like SPM cut
> out
> >> brain activity in the
> >> > OFC after first-level analysis.
> >> >
> >> > To resolve this issue, I am thinking of
> trying to
> >> force SPM to use an
> >> > explicit mask of the entire brain. Does
> anyone know
> >> how to implement
> >> > this in script format?
> >> >
> >> > Alternatively, if anyone has better ideas on
> how to
> >> improve signal in
> >> > the OFC, please let me know.
> >> >
> >> > Many thanks in advance for all your help!
> >> > Deborah Tang, Doctoral Candidate
> >> > McGill University
> >> > Montreal Neurological Institute
> >> > 3801 University St, Room WB 214D
> >> > Montreal, QC H3A 2B4
> >> > Canada
> >> >
> >> > Phone: (514) 398-6644 Ext. 089469
> >> > Fax: (514) 398-8948
> >> > [log in to unmask]
> >>
> >
> >
> >
>
>
>