On Mon, May 11, 2009 at 8:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Jeff Phillips wrote:

Hi Doug,

Thanks for responding, and I think I need to restate our original question(s). What we are trying to do is to get a metric of the reliability of retinotopic mapping--i.e., across multiple sessions, how often are regional borders replicated? To that end, we have been splitting up our data, treating pairs of eccen/polar stimulation runs (1 run eccen, 1 run polar) as separate sessions, and then summing the fieldsign maps which we get for each session. Thus, if we have 5 "sessions", we could ideally sum their fieldsigns and find that most vertices/voxels had a 5-out-of-5 score. I realize that our power over each session (i.e., over just two runs) is very low, but ignoring that very important issue for the time being, does it make sense to sum (not average) our fieldsign maps in this way?

Seems reasonable.

Relatedly, can you think of a scenario in which the V1 fieldsign could be opposite between two sessions, even if the direction of stimulation is the same (and consistently named in paradigm files)?

That seems unlikely, but I vaguely remember that I thought it would be a good idea to have the software adjust the sign such that the calcarine always had +1, implying that I ran into a situation where there was a flip, but I can't remember what that situation was. Jon, do you know?

doug

Thanks,

Jeff

On Mon, May 11, 2009 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Hi Y'all, sorry for not chiming in sooner. Jeff, if you have
multiple eccen or polar runs, you should just be able to set them
up as runs in the fsfast directory structure (ie, as dirs with
0-padded, 3digit run numbers), and it should find them and combine
them properly. And you can include the directionality in the
paradigm file, as you have suggested.

doug

Don Hagler wrote:

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.phillips@gmail.com
<mailto:jeffrey.s.phillips@gmail.com>
To: dhaglerjr@hotmail.com <mailto:dhaglerjr@hotmail.com>
CC: freesurfer@nmr.mgh.harvard.edu
<mailto: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
<dhaglerjr@hotmail.com <mailto:dhaglerjr@hotmail.com>
<mailto:dhaglerjr@hotmail.com <mailto:dhaglerjr@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.phillips@gmail.com
<mailto:jeffrey.s.phillips@gmail.com>
<mailto:jeffrey.s.phillips@gmail.com
<mailto:jeffrey.s.phillips@gmail.com>>
To: dhaglerjr@hotmail.com <mailto:dhaglerjr@hotmail.com>
<mailto:dhaglerjr@hotmail.com <mailto:dhaglerjr@hotmail.com>>

CC: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto: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
<dhaglerjr@hotmail.com <mailto:dhaglerjr@hotmail.com>
<mailto:dhaglerjr@hotmail.com

<mailto:dhaglerjr@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.phillips@gmail.com
<mailto:jeffrey.s.phillips@gmail.com>
<mailto:jeffrey.s.phillips@gmail.com
<mailto:jeffrey.s.phillips@gmail.com>>

To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto: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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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting