[Homer-users] Odd HRF shape: possible explanations?

Wed Mar 15 08:56:38 EDT 2017

Dear Felix,
   thanks again for your suggestions.

What do you mean exactly when you say to remove the trend of each trial
before doing the block-average?
hmrBlockAvg, which is the function that caculates the block average in
Homer2, automatically does detrend by removing the signal average over the
2 seconds before the stimulus onset (in my case). Is there anything else I
should do? And in that case, what Homer2 function should I use to do it?

I chose to filter using a band [0,1] Hz. However, even if I do filter with
a narrower band like [0.02, 0.5] Hz for example, the outcome doesn't change
much. I'd say that's pretty much the same.

I used 5 as DPF (for the head of newborns), as suggested in

Duncan, A., Meek, J.H., Clemence, M., Elwell, C.E., Tyszczuk, L., Cope, M.,
Delpy, D.T., 1995. Optical pathlength measurements on adult head, calf and
forearm and the head of the newborn infant using phase resolved optical
spectroscopy. Phys. Med. Biol. 40, 295–304.

Thanks,
Luca

On Tue, Mar 14, 2017 at 12:53 PM, Scholkmann Felix <Felix.Scholkmann at usz.ch>
wrote:

> Dear Luca,
>
>
>
> Thanks for the additional information.
>
> From what I see on the figures you send, you did not remove the trend of
> each trial before calculating the block-averages. This is not quite
> correct; the trend needs to removed properly in order to see the "real"
> hemodynamic response function. Also standard low-pass filtering is not
> optimal, it is necessary to apply a band-pass filter to that the
> high-frequency and low-frequency noise is removed. Otherwise you get
> hemodynamic responses that are heavily influenced by physiological noise.
>
> Also make sure that the correct DPF is chosen for the calculation of the
> hemodynamic signals (it is different in neonates).
>
>
>
>
>
> Kind regards,
>
> Felix
>
>
>
>
>
>
>
> *From:* homer-users-bounces at nmr.mgh.harvard.edu [mailto:
> homer-users-bounces at nmr.mgh.harvard.edu] *On Behalf Of *Luca Filippin
> *Sent:* Montag, 13. März 2017 16:31
> *To:* homer-users at nmr.mgh.harvard.edu
> *Subject:* Re: [Homer-users] Odd HRF shape: possible explanations?
>
>
>
> Thanks Felix for your comments and for the bibliography.
>
>
>
> We carefully selected the best babies so to reduce the impact of the
> movement artifacts.
>
> We applies a standard lowpass filtering (cut frequency at 1Hz) & signal
> correction. Homer removes from the analysis the stimuli around which the
> signals are too compromised.  Unfortunately we didn't measure any
> physiological confounds: heart beat, respiration etc.
>
>
>
> Best,
>
> L.
>
>
>
>
>
> On Sun, Mar 12, 2017 at 10:26 PM, Scholkmann Felix <
> Felix.Scholkmann at usz.ch> wrote:
>
> Dear Luca,
>
>
>
> From my own fNIRS studies done with neonates and from published papers I
> know that there are several factors that are causing the HRF of neonates
> being different compared to the HRF of adults:
>
>
>
> (1) Normaly, the amount of *movement artifacts* in fNIRS signals
> from neonates is larger compared to recordings from adults. This, in
> combination with the filtering, can cause distortions of the shape of
> the HRF. In oder to prevent this, all trials that are heavily contaminated
> with artifacts should be rejected. If the artifacts are not that severe the
> signal can be reconstructed. There are several methods available. For
> example, the algorithm published in 2010 [1] (I can send you the Matlab
> code if you need it), or other methods as implemented in NIRS-SPM and Homer.
>
>
>
> (2) According to findings from Chen et al. [2] *the neuro-vascular
> coupling comprises two components*: a fast and a slow mechanical change
> in the endothelium. The fast component (due to endothelial
> hyperpolarization) has a high propagation speed (about 2 mm/s), the slow
> one (due to calcium wave-associated dilation) propagated much slower. These
> two compoents form the shape of the HRF. In adults, these two mechanism
> work quite well - which is not the case in neonates. In
> neonates, one mechanis is well developed, the other not - as shown
> by Kozberg et al. [3]:
>
> *"Our data suggest that there are at least two vascular mechanisms at work
> in normal neurovascular coupling: (i) a global, delayed constriction
> process, present from early development and (ii) a localized initial
> hyperemia that develops gradually and is not in place at birth."*
>
> So, in neonates (depending on the age), the neuro-vascular coupling is
> different and will produce different HRFs than in adults.
>
>
>
> (3) fNIRS signals are *contaminated with physiological signals* coming
> from the extracerebral compartment (skalp blood flow) and
> systemic physiology affecting the global cerebral blood flow. See the
> review of 2016: [4]. CW-NIRS systems with only one source-detector system
> are susceptible to these artifacts.
>
> If there is a global changes in blood pressure, the fNIRS signals will be
> affeced. This is especially true for neonates - as nicely shown by Kozberg
> et al. [3]:
>
> *"We also observed that stimulus-evoked systemic blood pressure increases
> can cause apparent adult-like positive BOLD cortical responses in neonates
> consistent with immature autoregulation. We conclude that the parallel
> development and complex interplay of autoregulation, neurovascular
> coupling, and neuronal function in the developing brain should be carefully
> considered when interpreting hemodynamic measures such as fMRI BOLD in
> infants and children."*
>
> See also the figures in this paper that visualize the problem.
>
>
>
> (4) And finally, the shape of the HRF depends on the *type of filtering*
> applied. The main parameters are the lower and upper cutoff-frequencies of
> the bandpass-filter and the filter type (as well as the order of the
> filter). Changing these parameters will change the shapes. In addition, the
> shapes depend also on the choise of either using the mean or the median
> for calculating the block-averages. I recommend using the median.
>
>
>
> In summary, there are many factors involved causing "abnormal" HRF shapes
> in fNIRS recordings of neonates. It's a mixture of physiology and
> technology that determines how the shapes will look. The best was is to
> report precisely all the signal processing steps performed and to conduct
> additional physiological measurements (e.g. hear rate, SaO2, respiration
> rate, etc.) during the fNIRS experiments in order to allow a correct
> physiological interpretation of the fNIRS signals.
>
>
>
> Kind regards,
>
> Felix
>
>
>
> [1] http://iopscience.iop.org/article/10.1088/0967-3334/31/5/004/meta
>
> [2] http://jaha.ahajournals.org/content/3/3/e000787
>
> [3] https://www.ncbi.nlm.nih.gov/pubmed/23426630
>
> [4] http://neurophotonics.spiedigitallibrary.org/article.aspx?ar
> ticleid=2502725
>
>
>
>
>
>
>
>
> ------------------------------
>
> *Von:* homer-users-bounces at nmr.mgh.harvard.edu <
> homer-users-bounces at nmr.mgh.harvard.edu> im Auftrag von Cecile Issard <
> cecile.issard at etu.parisdescartes.fr>
> *Gesendet:* Sonntag, 12. März 2017 17:10
> *An:* homer-users at nmr.mgh.harvard.edu
> *Betreff:* Re: [Homer-users] Odd HRF shape: possible explanations?
>
>
>
> Hello Luca,
>
> What are the 40 s you average? Only one block? Or a block + silence? It
> seems to me that 50 to 80 ms is very short in between blocks.
>
> Best,
>
> Cécile Issard
> PhD student
> Laboratoire Psychologie de la Perception
> Université Paris Descartes- CNRS
> Paris, France
>
> Le 11 mars 2017 5:06 PM, Luca Filippin <luca.filippin at gmail.com> a écrit :
>
> Hi,
>
>    we've been using Homer2 to analyze some data collected on newborns and
> we get some puzzling HRF shapes as result, averaged over a 40 secs temporal
> window The function has in some cases multiple humps: it rises then
> descends a bit and then rises again, descends again and so on, 2 or more
> times. In some other cases it simply rises and doesn't fall at all.
>
>
>
> Would you have any explanations for that?
>
>
>
> We believe that it has something to do with the stimuli design.
>
>
>
> Our stimuli are sounds of variable length between 18 and 22 secs, roughly.
> Each sound is made of block of N repeated short sound segments (for
> example: BI), interleaved with other blocks of M sound segments of the same
> type BI, but shorter duration:
>
>
>
> N x BI (pause) M x shorter BI  (variable pause) N x BI (variable pause) M
> x shorter BI  (variable pause) ...
>
>
>
> where "variable pause" is a silent segment of duration between 50 and 80
> ms.
>
>
>
> We wonder if  there's a way to do the analysis so to disentagle the
> contribution of each block of sound segment within a sound stimulus. We
> play different sounds during the experiments: each sounds onset is
> separated by roughly 50 seconds. The problem would be perhaps, the
> estimation of the baseline.
>
>
>
> Many thanks for your help,
>
> Luca
>
>
>
>
>
>
>
>
>
>
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