Try changing line #381 in ReApplyFix/ReApplyFixPipeline.sh from:
ML_PATHS="addpath('${FSL_MATLAB_PATH}'); addpath('${FSL_FIX_CIFTIRW}');"
to
ML_PATHS="restoredefaultpath; addpath('${FSL_MATLAB_PATH}'); addpath('
${FSL_FIX_CIFTIRW}');"
-Keith
On Mon, Sep 11, 2017 at 5:54 PM, Sang-Young Kim <sykim...@gmail.com> wrote:
> Yes, I’m using CIFTI data. This is the interpreted version.
>
> Sang-Young
>
>
> On Sep 11, 2017, at 5:59 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
>
> Are you using CIFTI data? Is this the compiled version of matlab or the
> interpreted version?
>
> Peace,
>
> Matt.
>
> On 9/11/17, 4:19 PM, "hcp-users-boun...@humanconnectome.org on behalf of
> Sang-Young Kim" <hcp-users-boun...@humanconnectome.org on behalf of
> sykim...@gmail.com> wrote:
>
> Dear HCP experts:
>
> I¹m struggling with FIX for many days. The problem is that FIX does not
> generate cleaned data.
> So I found error message in .fix.log file as shown below.
> ****************************************************************
> TR =
>
> 1
>
> Elapsed time is 2.053048 seconds.
> {?Error using file_array/permute (line 10)
> file_array objects can not be permuted.
>
> Error in read_gifti_file>gifti_Data (line 191)
> d = permute(reshape(d,fliplr(s.Dim)),length(s.Dim):-1:1);
>
> Error in read_gifti_file>gifti_DataArray (line 122)
> s(1).data = gifti_Data(t,c(i),s(1).attributes);
>
> Error in read_gifti_file (line 45)
> this.data{end+1} = gifti_DataArray(t,uid(i),filename);
>
> Error in gifti (line 74)
> this = read_gifti_file(varargin{1},giftistruct);
>
> Error in ciftiopen (line 16)
> cifti = gifti([tmpname '.gii']);
>
> Error in fix_3_clean (line 48)
> BO=ciftiopen('Atlas.dtseries.nii',WBC);
> }?
> **********************************************************************
>
> Actually I saw many posts with the same error. But no clear solution is
> provided. I believe I set the path correctly and use last version of
> GIFTI toolbox. And I have tested "ciftiopen" function directly on the
> matlab. It worked in matlab.
> But I have no idea why above error came up while running FIX.
>
> Any insights would be greatly appreciated.
>
> Thanks.
>
> Sang-Young Kim, Ph.D.
>
> Postdoctoral Fellow
> Department of Radiology, University of Pittsburgh
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