Hi Satoru,
That's a reasonable request... both implicit and explicit masking. Try out
the attached spm_uc_FDR; it allows the masking to be specified in a 4th
form, Vm = {ImplicitMaskValue, ExplicitMaskVolHandle}. If it works for you
I'll update the SPM code base with these changes.
-Tom
On Tue, Feb 24, 2009 at 11:51 PM, Satoru Hayasaka <[log in to unmask]>wrote:
>
>
> Hi Tom,
>
>
>
> Thank you for clarifying that. It makes sense.
>
>
>
> Is there any way to use both an ROI mask image and the implicit zero
> masking? I noticed that, when spm_uc_FDR takes an ROI mask image as variable
> Vm, it doesn’t do implicit masking even though it does NaN masking. There is
> always a possibility for an ROI mask image to include implicitly masked
> voxels of the statistic image; in fact, this actually was the cause of the
> problem described in this thread. I erroneously assumed that implicitly
> masked voxels aren’t included in the calculation of the FDR threshold when
> an ROI mask is supplied, but I realized I was wrong. This problem may not be
> specific to PickAtlas, so I am wondering if there is any way to get around
> this situation without modifying the factory version of spm_uc_FDR.m. There
> might be other people using spm_uc_FDR function and a mask image without
> realizing this problem, so any hint would be helpful.
>
>
>
> Thanks,
>
> -Satoru
>
>
> ------------------------------
>
> *From:* SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] *On
> Behalf Of *Thomas Nichols
> *Sent:* Tuesday, February 24, 2009 3:46 PM
> *To:* [log in to unmask]
> *Subject:* Re: [SPM] wfu pickatlas problem?
>
>
>
> Hi Satoru,
>
>
>
> Just a follow up, there's no need to edit spm_uc_FDR. The change you made
> essentially 'locks on' implicit zero masking; instead, masking is meant to
> be specified with the last argument.
>
>
>
> For example, in spm_getSPM.m, the function is called as
>
> u = spm_uc_FDR(u,df,STAT,n,VspmSv,0);
>
> where the 0 argument is telling spm_uc_FDR to ignore zeros. See
> the usage for the full details...
>
> % Vm - Mask in 1 of 3 forms
> % o Scalar, indicating implicit mask value in statistic image(s)
> % o Vector of indicies of elements within mask
> % o Mapped mask image
> % (Ignored if Vs is a vector.)
>
>
>
> If you edit the PickAtlas calls accordingly you can use the
> factory-supplied spm_uc_FDR.m.
>
>
>
> -Tom
>
>
>
>
>
> On Tue, Feb 24, 2009 at 12:38 AM, Satoru Hayasaka <[log in to unmask]>
> wrote:
>
>
>
> First, let me apologize for a rather harsh tone of my language in my email
> below; it was meant to be an internal memo in our group but somehow it got
> posted on the SPM mailing list unedited.
>
>
>
> It turned out, the strange phenomenon described below is caused by a
> mismatch between the number of in-mask voxels between spm_uc_FDR.m and
> spm_P_FDR.m. You can correct this problem by editing a line in spm_uc_FDR.m
> function. Alternatively you can edit two lines in wfu_spm_getSPM5.m function
> to achieve the same result. The edited versions of both functions are
> attached. Either of these changes should correct the problem.
>
>
>
> Finally, being a statistician, I don’t think it’s a good idea to relax the
> threshold until you see a blob. I know some people do this, but changing the
> threshold after seeing the results doesn’t sound like a good science.
>
>
>
> -Satoru
>
>
> ------------------------------
>
> *From:* SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] *On
> Behalf Of *Simon Jones
> *Sent:* Monday, February 23, 2009 11:24 AM
>
>
> *To:* [log in to unmask]
> *Subject:* Re: [SPM] wfu pickatlas problem?
>
>
>
> Dear Satoru and Tom
>
>
>
> I had a similar issue as Wei-chun Wang.
>
>
>
> I have analyzed some data and using FDR 05 threshold within an ROI in the
> PickAtlas and receive no suprathreshold clusters. But subsequently using
> the standard SPM SVC clusters are detected.
>
>
>
> Page 1. Standard SPM analysis using uncorrected threshold p 001. Some
> coordinates appear to have an FDR significance < 05.
>
> Page 2. Standard SPM using FDR corrected threshold identifies the same
> coordinates.
>
> Page 3. Apply SVC to page 2 on an ROI results makes the FDR corrected
> values slightly more significant.
>
> Page 4. Same data using PickAtlas with the ROI in 3 and uncorrected
> threshold p 001. Similar results to 1.
>
> Page 5. Same data using PickAtlas with the ROI and FDR corrected threshold
> p 05 and no significant voxels are found.
>
>
>
> I think SPM SVC applies threshold to data already passed through to the
> results so the PickAtlas differs? If I pick a higher FDR threshold than
> 0.05 such as 0.1 then the significant voxels are reported by the PickAtlas
> with values like 0.034 etc. I attach a graph of the statistics similar to
> Satoru’s. The blue SPM FDR 05 crosses once, the red PickAtlas 0.05 do not
> cross (so no clusters found), the green PickAtlas 0.1 threshold actually
> crosses the red wiggly line 3 times ( the point at 114 is off the scale
> shown) so this time it finds clusters. What conclusions can be made? You
> can see in page 4 that some of the main blob is cut by the ROI. I am not
> trying to tweak thresholds.
>
>
>
> Thank you for your help
>
>
>
> Simon
>
>
>
>
>
> *From:* SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] *On
> Behalf Of *Thomas Nichols
> *Sent:* 23 February 2009 13:23
> *To:* [log in to unmask]
> *Subject:* Re: [SPM] wfu pickatlas problem?
>
>
>
> Dear Joe et al,
>
>
>
> In fact there's no problem with the plot of P-values starting above the
> line. For a level-alpha FDR procedure, all you need is one or more P-values
> that fall below the slope-alpha line, and the largest such P-value defines
> the FDR threshold. In statistics lingo, this Benjamini & Hochberg FDR
> method is a "step-up" test, which essentially works from worst P-value and
> steps 'up' until it finds a significant P-value and rejects that null and
> all others with smaller P-values; this is in contrast to a step-down test
> which starts from the most significant P-value, and and stops at the first
> non-significant P-value. (I'm Satoru remembers this, as we co-wrote a paper
> explaining the difference [1] :)
>
>
>
> Anyway, I can't help explain Wei-chun's problem, but wanted to clarify this
> issue.
>
>
>
> -Tom
>
>
>
> [1] Thomas Nichols and Satoru Hayasaka
>
> Controlling the familywise error rate in functional neuroimaging: a
> comparative review
>
> Statistical Methods in Medical Research 2003; 12: 419-446
>
>
>
> On Tue, Feb 10, 2009 at 9:52 PM, Joseph Maldjian <[log in to unmask]>
> wrote:
>
> Wei-Chung,
>
> Below is the response from Satoru Hayasaka in our group on your
> dilemma...
>
>
>
> So, Ben gave me a list of t-scores for this ROI, and I was able to
> figure out why this person got strange results. As I said yesterday, the
> FDR threshold is determined by plotting uncorrected p-values from the
> smallest to the largest. Then you draw a straight line corresponding the
> FDR value of your choice (0.05, 0.072, etc), and wherever the p-value
> curve crosses this straight line is the FDR threshold. See the attached
> figure for an illustration of this.
>
> Now, in order for the FDR threshold to exist, the p-value curve should
> start below the straight line, and crosses the straight line as it
> increases. Unfortunately, this person's p-value curve doesn't start
> below the straight line, so theoretically the FDR threshold is
> undefined, and nothing survives the FDR correction. But this person
> played with the FDR threshold value to cause a double-crossing (see
> yellow line). This, in no way, makes the FDR-corrected p-values valid;
> this FDR-threshold "fooled" (hopefully unintentionally) spm_P_FDR.m and
> made it produce invalid p-values. I guess whoever wrote spm_P_FDR.m
> wasn't prepared for a scenario like this.
>
> So, this is the answer to this conundrum. Nothing really survived; but
> this person tweaked the threshold and produced the results which are
> invalid and misleading. So, I guess you have to call a spade a spade.
> Nothing survived at FDR<0.05, and that's the end of the story. It has
> nothing to do with PickAtlas.
>
> -Satoru
>
>
>
> ------------------------------------------------------------------------
> Joseph A. Maldjian, MD
> Professor and Chief of Neuroradiology
> Director Advanced Neuroscience Imaging Research Core (ANSIR)
> Wake Forest University School of Medicine
> Office:336 716-2815
> fax: 336 716-2870
> email: [log in to unmask]
> website: www.fmri.wfubmc.edu/maldjian.htm
> ------------------------------------------------------------------------
> -
>
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
> On Behalf Of Wei-chun Wang
> Sent: Monday, February 09, 2009 7:38 PM
> To: [log in to unmask]
> Subject: [SPM] wfu pickatlas problem?
>
> I'm trying to use pickatlas with SPM and I'm running into a problem. I
> have
> a ROI that appears to be just under the threshold for significant after
> small volume correction (.049 FDR). However, when I use pickatlas and
> .05
> FDR as my threshold, my activation does not reach threshold. HOWEVER, if
> I
> use .072 FDR my activations show up, and in the table the corrected p
> value
> is properly listed as .05
> To sum, my problem is that the threshold has to be relaxed by ~.022 in
> order
> for the actual threshold (.05) to be seen by SPM.
>
> I've included 3 screen shots that illustrate my problem:
> "uncorrected" shows what happens if i set an uncorrected p-value and
> then
> use SPM's SVC function. you can see that the FDR corrected is .05
> "pickatlas_05" shows what happens if i use pickatlas and set the p-value
> to
> .05 FDR. no activations reach the threshold
> and finally, "pickatlas_072" shows what happens if i use pickatlas and
> set
> the p-value to .072 FDR. at this point it appears most of the
> activations
> that reach the .05 threshold appear.
>
> This isn't a rounding error. The activations do not show up if I try
> .051 or
> .06, only at .072. Also matlab shows that the FDR corrected p-value is
> ~.049. I was wondering if this is a bug in the software and if there is
> a
> workaround? Or is it a problem in my data? I was hoping to use this
> program
> in order to produce accurate activation maps of just the small volume
> corrected ROI. So alternatively, if anyone can recommend a separate
> method
> for doing so I would be quite appreciative.
> Wei-chun Wang
>
>
>
>
> --
> ____________________________________________
> Thomas Nichols, PhD
> Director, Modelling & Genetics
> GlaxoSmithKline Clinical Imaging Centre
>
> Senior Research Fellow
> Oxford University FMRIB Centre
>
>
>
>
> --
> ____________________________________________
> Thomas Nichols, PhD
> Director, Modelling & Genetics
> GlaxoSmithKline Clinical Imaging Centre
>
> Senior Research Fellow
> Oxford University FMRIB Centre
>
--
____________________________________________
Thomas Nichols, PhD
Director, Modelling & Genetics
GlaxoSmithKline Clinical Imaging Centre
Senior Research Fellow
Oxford University FMRIB Centre
