Tim, I just used three dots “...” to delete my complete folder path in the email I sent for privacy reasons. I’ll try the suggestion you mentioned.
Thanks for your help! Regards, Anita On Jan 17, 2019, at 5:10 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: 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<mailto: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<mailto:amsi...@wisc.edu> ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Thursday, January 17, 2019 4:27:17 PM To: Harms, Michael; Anita Sinha; hcp-users@humanconnectome.org<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Thursday, January 17, 2019 at 4:05 PM To: Anita Sinha <amsi...@wisc.edu<mailto:amsi...@wisc.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Anita Sinha <amsi...@wisc.edu<mailto:amsi...@wisc.edu>> Date: Thursday, January 17, 2019 at 3:37 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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. 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