I am not familiar with fsfast, so someone with intimate knowledge of
the code (Doug?) could help more. But if you can specify the stimulus
order in your paradigm files, then you should not have to do any phase
reversals yourself. It seems strange (i.e. bug-like) that your
fieldsign comes out different for the two sessions in this situation.
When you view the resulting polar angle and eccentricity maps in
tksurfer, are the colors reversed as well?
------------------------------------------------------------------------
Date: Mon, 11 May 2009 15:01:53 -0400
Subject: Re: [Freesurfer] Can fieldsigns be added across sessions?
From: jeffrey.s.phill...@gmail.com
To: dhagle...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Hi Don,
Thanks for writing back again. Let me clarify: in our last session,
we had a scanning menu like this:
1 run polar/clockwise
1 run eccen/expanding
1 run polar/counter-clockwise
1 run eccen/contracting
The difference in direction was reflected in our paradigm files
(*.par), with clockwise & expanding runs categorized as positive, and
the others as negative. I have assumed that if the paradigm files
specify this difference, it will not be necessary to manually flip the
signs for negative runs. Is this correct?
Jeff
On Mon, May 11, 2009 at 2:45 PM, Don Hagler <dhagle...@hotmail.com
<mailto:dhagle...@hotmail.com>> wrote:
1. Fieldsign is supposed to be -1 or 1, without values in
between. It is the sign of the cross product. I don't see why
you would want to average the fieldsign. You will get the best
estimate of the fieldsign by calculating it from the average of
all your available data.
2. Reversing the stimulus direction would definitely affect the
fieldsign calculation. And you will have to take it into account
if you average across scans or sessions. By that I mean you need
to reverse the phase (by setting the imaginary component negative)
of one direction before adding to the other. I also subtract a
few seconds worth of phase to account for hemodynamic delay.
3. The sign may be arbitrary, but it is not random. The fieldsign
depends on whether you consider clockwise a positive or negative
rotation and expansion positive or negative. If you change either
of those conventions, the fieldsign will flip. Also, the color
wheel in tksurfer depends on those conventions. Red is supposed
to be upper field and green is suppoed to be lower field. That
too is an arbitrary assignment, but it only holds true for
clockwise rotations. For counterclockwise, you need to reverse
the phase for the colors to look right.
4. Someone else may know if the fsfast tools can handle this type
of situation.
------------------------------------------------------------------------
Date: Mon, 11 May 2009 12:40:41 -0400
Subject: Re: [Freesurfer] Can fieldsigns be added across sessions?
From: jeffrey.s.phill...@gmail.com
<mailto:jeffrey.s.phill...@gmail.com>
To: dhagle...@hotmail.com <mailto:dhagle...@hotmail.com>
CC: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Hi Don,
Thanks for your comments. I will try operating on the
eccentricity and polar angle maps first--however, if I calculate a
fieldsign from average maps, I presume that the fieldsign map will
not be similarly graded, but rather binary. I'll have to think
about how to adapt that to our purposes.
I'm confident that the stimulus order was not reversed between
sessions. One difference which did exist was that the first
session involved unidirectional stimulation (i.e., only clockwise
wedges and only expanding rings), while the second session
involved bidirectional stimulation in alternating runs (i.e., both
clockwise/counterclockwise and expanding/contracting rings).
Would this difference create any problems?
More generally, I'm still a bit confused about the calculation of
the fieldsign. The wiki notes that "positive" and "negative" are
arbitrarily defined--in other words, these terms don't bear any
relation to clockwise/counterclockwise stimulation. It also
appears (but please correct me if I'm wrong) that the meanings of
these terms are not linked across the polar angle and eccentricity
manipulations--that is, I haven't read of any rule that says if
you call clockwise wedges positive, then expanding rings must also
be termed positive. I thought that knowing this directionality
would be important to interpreting the cross-product.
I have been unable to find a document, wiki page, etc. which
explains some of these details--if you happen to know of one, I
would appreciate the reference.
Thanks,
Jeff
On Fri, May 8, 2009 at 3:32 PM, Don Hagler <dhagle...@hotmail.com
<mailto:dhagle...@hotmail.com>> wrote:
I think you should average your polar angle and eccentricity
maps across session and then calculate fieldsign from that.
You do a complex average (a separate average for real and
imaginary components).
By the way, the sign of the fieldsign measure should have a
fixed meaning; the orientation of the cross product of the
gradients of polar angle and eccenctricity, relative to the
cortical surface. Are you sure you didn't reverse the
stimulus order or something? Was the projector's image upside
down or flipped left/right?
------------------------------------------------------------------------
Date: Thu, 7 May 2009 18:47:32 -0400
From: jeffrey.s.phill...@gmail.com
<mailto:jeffrey.s.phill...@gmail.com>
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Can fieldsigns be added across sessions?
Hi all,
I would like to add fieldsigns across multiple retinotopy
sessions in the same subject, in order to get a metric of the
reliability of the mapping. However, when I tried to do this
in one subject, I found that fieldsigns from two sessions
largely canceled one another out. This led to a discussion in
our lab of whether the fieldsign 1) has a consistent meaning
across sessions and subjects, or 2) whether the fieldsign in a
given region, say V1, may switch from positive to negative due
to noise or between-subject differences. For example, a
colleague speculated that paint-sess could start with +1 at an
arbitrary starting point on the edge of an occipital patch,
then flip the sign whenever the polar angle/eccentricity
gradients reversed themselves. Thus, V5 might be +1, V4 = -1,
V3 = +1, V2 = -1, and V1 would be +1. However, if noise in a
given session resulted in a failure to detect V4, then V1
would end up being the opposite fieldsign, -1. Is this
correct? If so, then I might be shooting myself in the foot
by adding fieldsign maps from different sessions. I would
really appreciate any insight about how the fieldsign is
assigned, and whether circumstances like the ones I describe
could cause it to flip for a given functional region.
Thanks,
Jeff Phillips
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