I found the following error, please advice: (before is giving me some warnings
about different functions that has same name as a Matlab builtin, I have pasted
the output from last warning and first error).
Which are the files that needs to be included in ‘CIFTIMatlabReaderWriter’ for
the settings.sh?
Warning: Function subsref has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.
> In path (line 109)
In fix_3_clean (line 45)
/bin/bash: /usr/local/workbench/bin_macosx64: is a directory
Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file
/private/var/folders/j2/__433pcd02l1cw9qkydkqs5h0000gn/T/tp6555679429695603.gii
failed.
Error in gifti (line 71)
this = read_gifti_file_standalone(varargin{1},giftistruct);
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 46)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Thanks!
-L
> On May 26, 2018, at 6:55 PM, Marta Moreno <[email protected]> wrote:
>
> You were right, now the problem is gone but still cannot find my
> clean.dtseries
>
> Here is the output, I could not find any error in .ica folder:
> hcp_fix RS_fMRI_1.nii.gz 2000
> processing FMRI file RS_fMRI_1 with highpass 2000
> running highpass
> running MELODIC
> running FIX
> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
> create edge masks
> run FAST
> registration of standard space masks
> extract features
> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using
> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and
> threshold 10
> FIX Applying cleanup using cleanup file:
> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set
> to 1
>
> Please advice.
>
> Thanks!
>
> -L
>
>
>> On May 26, 2018, at 2:52 PM, Glasser, Matthew <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> Perhaps you are running out of memory.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <[email protected]
>> <mailto:[email protected]>> on behalf of Marta Moreno
>> <[email protected] <mailto:[email protected]>>
>> Date: Saturday, May 26, 2018 at 1:50 PM
>> To: HCP Users <[email protected]
>> <mailto:[email protected]>>
>> Subject: [HCP-Users] error running hcp_fix
>>
>> Dear experts,
>>
>> I am getting the following error. Please advice:
>>
>> hcp_fix RS_fMRI_1.nii.gz 2000
>> processing FMRI file RS_fMRI_1 with highpass 2000
>> running highpass
>> running MELODIC
>> running FIX
>> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica
>> create edge masks
>> run FAST
>> registration of standard space masks
>> extract features
>> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using
>> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and
>> threshold 10
>> FIX Applying cleanup using cleanup file:
>> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set
>> to 1
>> sh: line 1: 10513 Killed: 9
>> /Applications/MATLAB_R2017b.app/bin/matlab -nojvm -nodisplay -nodesktop
>> -nosplash -r "addpath('/usr/local/fix1.065');
>> addpath('/usr/local/fsl/etc/matlab'); fix_3_clean('.fix',0,1,2000)" >>
>> .fix.log 2>&1
>>
>> Thanks,
>>
>> -L
>>
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