error in using wb_command inside matlab

[amirka1379]

I want to do a palm analysis with -transposedata and etc
but it keeps giving me 'Currently cannot read/write CIFTI files without the HCP Workbench'
I tried some of the ways you have mentioned to how to fix this problem but it did not help
I would appreciate it if you helped me how to use the hcp workbench inside Matlab
and how to work with the wb_command function
wb_view function is alright in Matlab
but my windows Matlab can not recognize wb_command with the system('wb_command')

[andersonwinkler]

Hi Amirhosein,

PALM uses the command "which" to locate programs such as wb_command, but this only works on Linux and Mac.

For Windows you'd have to edit the palm_checkprogs.m to make PALM set "palm_extern.wb_command = true" always, and further, edit palm_ciftiread.m and palm_ciftiwrite.m such that the variable "wb_command" is set at the beginning to point to the location in your system where the actual wb_command is located.

It should work then, but you'll have to make these edits by hand.

All the best,

Anderson

[amirka1379]

thanks a lot for your help i did succeed in running the command but I get this error after the first problem was solved
ERROR: NAME OF FILE: results_Y4h4Ng.gii

Output stream for external file reports its status as bad.

Error using xml_parser
The XML document was not valid

and when I do
gii = gifti('results_Y4h4Ng.gii');

this error will pop up
Error using xml_parser
The XML document was not valid

Error in gifti_read (line 14)
t = xml_parser(filename);

Error in gifti (line 105)
this = gifti_read(varargin{1},giftistruct);

[gllmflndn]

Hello @amirka1379
Assuming the file is where it should be when read by the gifti library, could you attach file results_Y4h4Ng.gii to this issue so that I can have a look?

[amirka1379]

results_Y4h4Ng.gii.zip
Thanks for your precious help this is the zipped file of it

[gllmflndn]

Thank you, the XML file is indeed not valid, two end tags are missing at the end of the file:

</DataArray>
</GIFTI>

After adding them manually, the file is parsed correctly so it might be worth checking whether there is an issue upstream with wb_command: are you using the latest version?
The data are stored in results_Y4h4Ng.gii.data: there might be further issues in reading the data but it would be good to clear the issue above first.

[gllmflndn]

I also notice the Data tag is missing so what actually needs to be added at the end of the file is:

  <Data/>
  </DataArray>
</GIFTI>