Try doing:
system('<whatever_path>/wb_command');
Except using the exact string you are providing to ciftiopen's second
argument. You should get the usage information for wb_command if the path
is correct and things are working.
Tim
On Thu, Jan 17, 2019 at 4:38 PM Anita Sinha <amsi...@wisc.edu> wrote:
> Matt/Michael,
>
>
> When I run g = gifti, I get g = gifti object 1-by-1. I have confirmed that
> I have the correct file paths to the wb_command, however, it seems to
> duplicate part of a file path string, which is why it cannot find the file.
> Is this a known issue?
>
>
> This is what I'm running:
>
>
> y = '/.../.../CM.dtseries.nii';
> ciftiFile = ciftiopen(y,'Z:/.../workbench/bin_windows64/wb_command');
> CM = ciftiFile.cdata;
>
> and receive the same error:
>
> Error using read_gifti_file_standalone (line 20)
> [GIFTI] Loading of XML file
> C:\Users\AMS217\AppData\Local\Temp\tp366ef3da_4687_4d6e_9b4a_bb7f0ce6fd8e.gii
> failed.
>
> Error in gifti (line 100)
> this = read_gifti_file_standalone(varargin{1},giftistruct);
>
> Error in ciftiopen (line 34)
> cifti = gifti([tmpfile '.gii']);
>
>
> Do I need to convert it to char or something so it is read in correctly?
>
>
> Regards,
>
>
> Anita Sinha
>
> Biomedical Engineering Graduate Student
>
> University of Wisconsin-Madison
>
> amsi...@wisc.edu
> ------------------------------
> *From:* Glasser, Matthew <glass...@wustl.edu>
> *Sent:* Thursday, January 17, 2019 4:27:17 PM
> *To:* Harms, Michael; Anita Sinha; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] CIFTI to Matlab
>
> That could also be due to it not finding the file or not finding
> wb_command.
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms,
> Michael" <mha...@wustl.edu>
> Date: Thursday, January 17, 2019 at 4:05 PM
> To: Anita Sinha <amsi...@wisc.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] CIFTI to Matlab
>
>
>
> Hi,
>
> It sounds like you don’t have the gifti library properly installed.
>
>
>
> Within matlab, what happens when you type
>
> g = gifti
>
>
>
> Do you get a gifti structure?
>
>
>
> Cheers,
>
> -MH
>
>
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> -----------------------------------------------------------
>
> Associate Professor of Psychiatry
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave. Tel: 314-747-6173
>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
>
>
> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Anita Sinha <
> amsi...@wisc.edu>
> *Date: *Thursday, January 17, 2019 at 3:37 PM
> *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> *Subject: *[HCP-Users] CIFTI to Matlab
>
>
>
> To Whom It May Concern,
>
>
>
> I am attempting to open up a dtseries.nii CIFTI file into Matlab to
> extract the time series matrix from rs-fMRI data. I have downloaded
> workbench and gifti-1.8 and am following the directions outlined in
> https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63963178 in
> #2 "How do you get CIFTI files into Matlab, but it isn't working.
>
>
>
> When I run this command:
>
> cii = ciftiopen('path/to/file','path/to/wb_command'); CIFTIdata = cii.cdata
>
>
>
> with the appropriate file paths, I keep receiving this error:
>
>
>
> Error using read_gifti_file_standalone (line 20)
>
> [GIFTI] Loading of XML file
> C:\Users\...\AppData\Local\Temp\tp904b5934_f040_4259_8a21_0b10e15aecc8.gii
> failed.
>
>
>
> Error in gifti (line 100)
>
> this = read_gifti_file_standalone(varargin{1},giftistruct);
>
>
>
> Error in ciftiopen (line 34)
>
> cifti = gifti([tmpfile '.gii']);
>
>
>
> I have added workbench and gifti to the path and saved everything in the
> same directory to mitigate file directory mismatch, but cannot past this
> error.
>
>
>
> Could you provide some help on how to resolve this?
>
>
>
> Thank you for your time.
>
>
>
> Regards,
>
>
>
> Anita
>
> _______________________________________________
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> of this information is strictly prohibited. If you have received this email
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