[ningfei]

HI Mike,

Sorry to know that you also have the problem. But since I can’t reproduce the problem from my side, it would be nice if you can send me a sample data with which you got the above error (of course if it’s okay to share the data). I may then test it here to find a possible solution for that.

Best,
Ningfei

[ningfei]

Hi Xiaoyu,

I am afraid the manual is not updated regarding the macaque toolbox. But if you have subscribed our newsletter, you probably already got noticed that we introduced a new “Space” function in LEAD, with which you can easily switch between different spaces, including the MNI Macaque space or even your own customized space. Just click the “Space ” menu you will see all the options in the “Change current space to” submenu. It will download the needed dataset automatically if not present.

Best,
Ningfei

[ningfei]

Hi Marcelo,

Please extract this into lead\ext_libs\ANTs (overwrite the old ones) and try again to see if it works.

Best,
Ningfei

[ningfei]

Hi Marcelo,

Seems it’s possibly an known issue of ITK which is used by ANTs. I will check it later and maybe there’re some ways to work around it.

Best,
Ningfei

[ningfei]

Hi,

ea_tonemapct_file is called after the normalization is done. If you saw the above error. It means that the normalization step did not finish correctly. Please check the log before the error to see if there is something wrong there.

Best,
Ningfei

[ningfei]

Cool that it works now :)

Best,
Ningfei

[ningfei]

Hi Xiaoyu,

As was recommended, you’d better use a recent MATLAB (later than R2014b) to run LEAD. This not only solves the problem you saw now: there’s a lot of graphic handling changes since version R2014b, which we’d adopted in LEAD, you may also encounter other problems if you use a lower version of MATLAB.

Best,
Ningfei

[ningfei]

Hi Vinny,

Did you upgrade LEAD from an old version without downloading the data updates or the full version? Since this pca.nii file had been added to LEAD some versions before. If so, you can get the file here. Or you may want to download the full data pack here.

Best,
Ningfei

[ningfei]

Hi Vinit,

The group connectome data has already been uploaded. You can try to download it now. It’s a large zip file with about 3GB, would take some time to finish. Alternatively, you can download it with your browser from here, if the downloading from matlab is not stable enough. And the extract the zip into the folder lead/connectomes/dMRI/.

Best,
Ningfei

[ningfei]

And the groupconnectome data is still on the way. Will let you know when it’s ready.

[ningfei]

Hi Vinny,

Sorry to know the problem is still there. But actually the message you saw there was a false alert. You should have already seen some other messages in the matlab command window, which said something like “Extracting code…” and “Copying new code…”. And you will have a tmp folder under lead. I fixed this issue just now. You can delete the tmp folder under lead and click the ‘Apply Hotfix’ menu again. You will still see the error message as before, but no more for next time. Hopefully everything will be fine from now on. Just a hint, the hotfix package is basically updated daily (if there’s new commit on github) before a new release coming. You could try it if you get problems, maybe it’s already fixed on github but not released yet.

Best,
Ningfei

[ningfei]

Hi Vinny,

Thanks for reporting us the problem you encountered. The error was just fixed on github. You could either pull if you are using github version of lead or click the ‘Install –> Apply Hotfix’ menu if you are using download version. However, it seems tha the group connectome file on our server was corrupted for some reason. I would let know you after we fix it. You could then try to download it again.

Best,
Ningfei

[ningfei]

Hi Mevleut,

Sorry to know that you have problem using LEAD. But you don’t actually need to install the “macaque toolbox” to use the Group Connectome. The “macaque toolbox” is already deprecated and replaced by “MNI_Macaque” space if you are using the latest version of LEAD v1.6.1.1 where space switching is introduced. Though the download menu is still there in the LEAD interface.

More detailed information (for example the error log) would be helpful to solve your problem.

[ningfei]

No problem. Good to know you solved it :)

[ningfei]

Hi Philip,

It’s really weird that dir([directory,options.prefs.prenii_searchstring]); return an empty cell. Could you check the value of directory and also paste here? If your images are under the directory folder, pfcell should not be empty as I see.

Best,
Ningfei

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