Cannot run the code

[suwangcn]

I cannot run the code even I did all the preparation correctly.

[dhino2000]

In which section did the error occur? I could run it all the way through with the sample data.

[suwangcn]

Hi,

Thank you for your response. Just the first step. When I opened SHARCQ, the window called UI Figure appeared. Then I clicked the button "Pre-Process Image", the error I published on github happened. I am using matlab R2020b, so I don't know if the version cause the problem in the functions.

Best,

Su

On Thu, May 12, 2022 at 11:12 PM dhino @.***> wrote:

In which section did the error occur? I could run it all the way through with the sample data.

— Reply to this email directly, view it on GitHub https://github.com/wildrootlab/SHARCQ/issues/6#issuecomment-1125614382, or unsubscribe https://github.com/notifications/unsubscribe-auth/APQSCD6DFXV2BGXUMARJNRLVJXCBLANCNFSM5VYSP3HA . You are receiving this because you authored the thread.Message ID: @.***>

[dhino2000]

Maybe, this problem is same as #4 issue, please see the trouble shooting and try again. (https://github.com/wildrootlab/SHARCQ/wiki/9.-Troubleshooting)

[krislauridsen]

Hi,

Could you try to redownload the code folder from the repository and see if a recent update fixes your bug?

Thanks

[ahmoberly]

Hello! I'm actually getting the same error stemming from that natsortfiles function (line 135). Is there a quick solution?

Thanks!

[krislauridsen]

Ensure that the master SHARCQ folder is added to your MATLAB path before compiling

[cesaracevedotriana]

Hi,

I've had the same error than was mentioned in the issue, during the first part of the image pre-processing. I cannot find the solution in the troubleshooting and I've added to the main path the SHARCQ master folder. Follow the image

[marhmue]

I encountered this same issue. I went through the raw .csv files outputted as intermediates, and found that troubles lay in negative values which are later used for indexing. I changed the code as follows (lines 39-40 in the screenshot below) in the function Warp_ROI, which seemed to fix things! However, I'm not sure if doing so may have other detrimental effects. Would you envision any?

[marhmue]

The above being said - I have not yet been able to make it through the entire SHARCQ paradigm with my coronal images. During the Image-ROI-Atlas-Composite stage (I've tried with both the Allen and Chon atlas), recognised cells seem to be misaligned. I've spent a few days troubleshooting, to no avail. I've looked through raw and transformed cell count/coordinate data, ROI files, transformed ROI files etc. both for my image sets and in comparing these to your test images provided. I've attached a screenshot which shows the error I'm encountering.

Is this something which you've seen or had happen in the past? Any advise or insight as to how this might be fixed would be deeply appreciated. Thank you for your time and consideration.