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Editing stim marks and Data type index

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Posts: 6
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Joined: 2 years ago

Hello everyone,

I am using Homer3, v1.33 on Matlab version 2021b on a Macbook. I have 2 questions:

Q1 (task description below): Is there a way to label my stimuli as test and silent conditions, so that I only calculate HRF for the test stimuli? I came across a tutorial on Homer that suggested dragging the mouse over the stimulus and toggling it on/off, but selecting will not be feasible as I have over 100 stim marks/triggers in the stimulus window. I also changed the amplitude value of those stimuli from 1 to -1 and saved it to the original file, but this didn’t turn off those stim marks either (it didn’t turn to dashed line).

Q2: After I run the analysis pipeline, it generated a matlab file for each participant in the ‘HomerOutput’ folder. In one of the cells in the dvAvg measurement list, there are 3 different outputs labelled as data type index (1,2,3).
What are these data type index? It is not similar to HbO or other types of concentrations, so I am not sure what these data type indexes mean.

Task description for Question 1: In this task, participants heard a nonword plus a sound and they were instructed to delete the sound from the word and say the word again. There were 65 stimuli presented, out of which 15 were silent conditions (i.e., there was no sound played and no response was made). We used EPrime to program the task and it sent triggers at the beginning and end of each stimulus but there was no way to label the test and silent conditions in the EPrime (because the presentation of both types of stimuli was random).

Thank you!!

3 Replies
Meredith Pecukonis
Posts: 16
Active Member
Joined: 2 years ago

Hi! I am also having a similar issue: when I change the amplitude value from 1 to -1 in the third column of and saved it to the snirf file, the stim marks don't seem to be turned off (they dont show up as dashed lines in Homer GUI. Are these stimulus trials removed from processing or not? If not, what is a simple was to remove/toggle off "bad" trials that I don't want to be processed?

Stomb Buddie
Posts: 1
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Joined: 4 months ago

Hello. I have the same problem with newer generation hardware. Will the same solution be used? I am not a specialist in this field, just starting out.

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Yuanyuan Gao
Posts: 5
Active Member
Joined: 2 years ago

Hi, thanks for posting this!
Q1 : Unfortunately it is not possible to select one stim mark type and assign a label to all its incidences in homer3. In homer3, you need to do it trial by trial.
The alternative way is to delete the markers in snirf file and save it (which needs some Matlab coding. I have put an example below).

%% add Homer3 path first, then run the code below

snirf = SnirfClass('2022-08-11_005.snirf'); % change the file name to your snirf file name

snirf.stim([1,4]) = []; % delete all the markers in stim type 1 and 4
snirf.stim(1,1).name = 'Active'; % rename stim
snirf.stim(1,2).name = 'Passive'; % rename stim

snirf.Save('2022-08-11_005_cleanstim.snirf') % save it to a new snirf file

Q2: Please refer to 'dataTypeLabel' (For example, output.dcAvg.measurementList(1).dataTypeLabel), which specifically indicates whether it is HbO/R or T. 

Let me know if you have further questions.