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[Solved] Issue Converting nirs to snirf files on Homer3

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Mitchell Holmes
Posts: 3
(@mgh1394)
New Member
Joined: 2 months ago

Hello,

 

I am from the same lab as tthuynh. We are having the same problem with some new data we have collected in which we are unable to convert some .nirs files to .snirf files. 

On MatLab, after we input the command "Homer3," we're finding that only some of our files are being converted and we are presented with the error message: FAILED error check: [FILENAME] will not be added to data set. It gives no further information. 

We can't seem to find a pattern as to why certain files won't be converted, but this is what we do know:

- All raw files (before we do any trimming of messy data) convert from .nirs to .snirf

- Files that have been trimmed or segmented into multiple files are a hit or miss (sometimes they convert, and sometimes they don't).

It seems clear that trimming the data is somehow making certain files unable to convert, however, there's nothing to distinguish why some trimmed files convert and why some don't - they all undergo the same processes before trying to convert with Homer3. 

I was wondering if you ever figured out a reason as to why this might be, and if you did, any information on how to move forward would be greatly appreciated. Thank you!!!

 

MH

 

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Meryem Yücel
Posts: 141
Admin
(@mayucel)
Estimable Member
Joined: 3 years ago

@mgh1394, what is the trimming procedure you apply? Are you using the segment snirf file feature of homer3 GUI or you do it offline yourself? 

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Mitchell Holmes
(@mgh1394)
Joined: 2 months ago

New Member
Posts: 3

@mayucel We have been trimming them with oxysoft. My procedure is as follows:

1. Collect data via oxysoft (creating a .oxy4 file)

2. trim the data via oxysoft offline

3. convert the now trimmed .oxy4 file to .nirs file via MatLab

4. convert .nirs file to .snirf file by typing command "Homer3" in MatLab - this is where the problem is, in that when Homer3 opens from here it only finds certain .nirs files to convert to .snirf

 

I hope this makes sense!

 

MH

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Meryem Yücel
Posts: 141
Admin
(@mayucel)
Estimable Member
Joined: 3 years ago

Instead, can you try first converting the raw to snirf and then segment them using homer segment tool? 

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Mitchell Holmes
(@mgh1394)
Joined: 2 months ago

New Member
Posts: 3

@mayucel That worked! Thank you so much for the help!

MH

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Meryem Yücel
Posts: 141
Admin
(@mayucel)
Estimable Member
Joined: 3 years ago

Awesome, glad to hear!

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