NITRC Hitachi2nirs Forum: open-discussion

RE: Why there isnomarksafter transfering hitachi to nirs file?

Rebecca Dewey — Fri, 02 Dec 2022 9:50:25 GMT

Brilliant, thanks so much Tingting!

Rebecca

RE: Why there is nomarksafter transfering hitachi to nirs file?

tingting — Fri, 02 Dec 2022 2:03:24 GMT

Hi Rebecca,

Thank you very much! I thought it is only possible to add markers manually in Homer3 if the markers were not imported automatically.

But indeed there is a way to "import" markers from aux. I am pointing it out here just in case anyone needs it.
That is, go to the "[b]Tools[/b]" column and select "[b]Edit Stimulus[/b]", then "[b]preview[/b]" aux and add markers.

Thank you again for your help.

Best,
Tingting

RE: Why there is nomarksafter transfering hitachi to nirs file?

Rebecca Dewey — Thu, 01 Dec 2022 9:32:51 GMT

Ok, good that you have an aux variable. I have not used Homer3, but I remember in Homer2 there used to be a way to "import" markers from the aux variable. It was just a couple of clicks and simple to do. Can you find anything like that in Homer3?

RE: Why there is no marksafter transfering hitachi to nirs file?

tingting — Thu, 01 Dec 2022 5:53:28 GMT

Hi Rebecca,

Thank you very much for your reply! Yes, I saw the "aux" variable when I open the nirs file in Matlab.

However, I opened the .nirs file in Homer3, which convert the .nirs file into .snirf file automatically, then I did not see any markers in Homer3 (please find an image of it).
Can you please let me know what should I do to show the markers? Thank you a lot!

Best,
Tingting

Why there is no marksafter transfering hitachi to nirs file?

Rebecca Dewey — Wed, 30 Nov 2022 9:49:22 GMT

I believe the markers should be saved into a variable named "Aux" - can you see this when you open the nirs file in Matlab?

Cheers,

Rebecca

Why there is no marks after transfering hitachi to nirs file?

tingting — Wed, 30 Nov 2022 8:13:12 GMT

I have run the script hitachi2nirs.m created by Rebecca Dewey in Matlab. I chose not to remove the mark (Do you want to remove the marker at the end of each stimulus? y/n: n) during the processing.

However, when I import the .nirs file (automatically converted to .snirf file) in Homer 3, there are no markers at all.

Did anyone experience this problem? It would be great if there is any implications. Fully appreciated with any help!

RE: Error: invalid datamatrix (d)

Rebecca Dewey — Wed, 15 Jun 2022 16:27:42 GMT

Thank you for reaching out. I have often seen this error when people are trying to use the wrong output file from the Hitachi software. You need to use the Probe1_MES file containing the raw intensity data, and not any of the calculated chromophore files.

Does this help at all?

Rebecca

Error: invalid datamatrix (d)

Shi Zhengwei — Fri, 10 Jun 2022 4:05:25 GMT

After using Rebecca Deweys script to convert Hitachi ETG 4000 data to the *.nirs format,my installation of Homer2 (on Matlab R2013a) does not open the file, but gives me an error message saying 1. Error: invalid datamatrix (d), it opens the Sample files though.Can you please help me solve this issue?
Thanks Again!

RE: How to choose the .POS file

Shi Zhengwei — Fri, 10 Jun 2022 3:33:18 GMT

Thanks for your help. I will try this way!

RE: How to choose the .POS file

Rebecca Dewey — Mon, 06 Jun 2022 8:58:54 GMT

Hello, you will need to create one pos file with all the optode locations in. The most genuine way to do this is by using a localiser to create one based on the real-life locations of the optodes. However, if you just want to conveniently visualise the data, you can easily start experimenting with the most helpful orientation for this by copying and pasting the locations from one pos file into the other, updating the optode numbers in sequence, and off-setting all the optodes in one array by a fixed amount in one dimension (e.g., adding 12 cm to the x dimension for all the optodes in the 4x4 array while leaving the 3x5 array as it is.

Good luck!
Rebecca