Sorry, one additional question: per your suggestion, I can handle adding/averaging the real and imaginary component masks, but what syntax can I use in paint-sess to convert those composite masks into fieldsign maps?

Thanks,

Jeff

On Mon, May 11, 2009 at 12:40 PM, Jeff Phillips < jeffrey.s.phillips@gmail.com> wrote:

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 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 To: 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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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 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 To: dhaglerjr@hotmail.com CC: 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 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 To: 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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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 To: dhaglerjr@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 <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>
To: dhaglerjr@hotmail.com <mailto:dhaglerjr@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 <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>
    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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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
greve@nmr.mgh.harvard.edu <mailto: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
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I was just going to average the field sign over the calcarine and multiply all vertices by -1 if that average came up negative. I can't remember what example made me think this was necessary. I remember seeing changes in the sign, but I can't remember whether it was subject-specific or if it changed from run to run.

doug

Jeff Phillips wrote:

Hi Doug and Jon,

I wanted to follow up on your last e-mail--can you tell me how you were able to set an "anchor point" in the calcarine fissure? If you can recall why it seemed necessary to set the calcarine fissure fieldsign to +1, I would greatly appreciate it. This sounds potentially useful to us, as it seems like some combination of low statistical power and the operation of the fieldsign algorithm could be causing the between-session inconsistencies in our maps.

Thanks,

Jeff

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