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 ------------------------------------------------------------------------ Windows Live™: Keep your life in sync. Check it out. <http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009> ------------------------------------------------------------------------ Hotmail® has a new way to see what's up with your friends. Check it out. <http://windowslive.com/Tutorial/Hotmail/WhatsNew?ocid=TXT_TAGLM_WL_HM_Tutorial_WhatsNew1_052009>
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