In your FSL FIX installation, you can try making the same change in line
#307 of call_matlab.sh
-Keith
On Mon, Sep 11, 2017 at 6:34 PM, Sang-Young Kim <sykim...@gmail.com> wrote:
> I am running the script ${HOME}/projects/Pipelines/ICAFIX/hcp_fix.
>
> Is there a point to modify the script in order for working FIX?
>
> Thanks.
>
> Sang-Young
>
>
> On Sep 11, 2017, at 6:28 PM, Keith Jamison <kjami...@umn.edu> wrote:
>
> Try changing line #381 in ReApplyFix/ReApplyFixPipeline.sh from:
>
> ML_PATHS="addpath('${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
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
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>>
>
>
>
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