help
help > CONN error during Preprocessing
May 24, 2019 08:05 PM | Carrie Brown - Holland Computing Center - University of Nebraska
CONN error during Preprocessing
Hello,
We have a user who is attempting to move their workflow over to our HPC system. Currently, she runs her analysis on her personal machine and it completes successfully using MATLAB r2017a spm12 and CONN 18a
We have installed the necessary software on our system and are attempting to run her scripts using MATLAB r2018b, spm12 and CONN 18b.
However, when running `conn_batch()`, we are getting errors that we cannot seem to solve. Can you give us some insight on why this may be happening and how we can correct?
Here is the MATLAB script that is being used (note: we ensured the paths are accurate and the necessary files exist)
And the error we are encountering is as follows:
We have a user who is attempting to move their workflow over to our HPC system. Currently, she runs her analysis on her personal machine and it completes successfully using MATLAB r2017a spm12 and CONN 18a
We have installed the necessary software on our system and are attempting to run her scripts using MATLAB r2018b, spm12 and CONN 18b.
However, when running `conn_batch()`, we are getting errors that we cannot seem to solve. Can you give us some insight on why this may be happening and how we can correct?
Here is the MATLAB script that is being used (note: we ensured the paths are accurate and the necessary files exist)
spm('defaults','fmri');
spm_jobman('initcfg');
Runs = {'Rhyme1'};
% for Run_no = 1:length(Runs)
Datapath = '/work/nl3wanglab/avantika';
BATCH.filename = fullfile(Datapath, SubId, strcat(SubId,'_conn_project.mat'));
% Batch Setup
BATCH.Setup.nsessions = 1;
BATCH.Setup.RT = 1;
BATCH.Setup.acquisitiontype=1;
BATCH.Setup.functionals{1}{1} = fullfile(Datapath, SubId, strcat(SubId,'_',Runs,'.nii'));
BATCH.Setup.structurals{1} = fullfile(Datapath, SubId, strcat(SubId,'_T1.nii'));
BATCH.Setup.outputfiles=[1,1,0];
% Batch Preprocessing
BATCH.Setup.preprocessing.art_thresholds(1)= 9;
BATCH.Setup.preprocessing.art_thresholds(2)= 4;
BATCH.Setup.preprocessing.template_structural = '/work/nl3wanglab/avantika/nihpd_sym_04.5-08.5_t1w.nii';
BATCH.Setup.preprocessing.template_functional = '/work/nl3wanglab/avantika/nihpd_sym_04.5-08.5_t1w.nii';
%BATCH.Setup.preprocessing.tpm_ngaus = [2 2 2 4];
BATCH.Setup.preprocessing.voxelsize_anat = 1;
BATCH.Setup.preprocessing.voxelsize_func = 2.5;
BATCH.Setup.preprocessing.boundingbox = [-90,-126,-72;90,90,108];
BATCH.Setup.preprocessing.FWHM = 8;
BATCH.Setup.preprocessing.coregtomean = 1;
% Direct Normalization
BATCH.Setup.preprocessing.steps = {'functional_realign&unwarp', 'functional_center','functional_art','functional_segment&normalize_direct','structural_center','structural_segment&normalize','functional_smooth'};
conn_batch(BATCH);
spm_jobman('initcfg');
Runs = {'Rhyme1'};
% for Run_no = 1:length(Runs)
Datapath = '/work/nl3wanglab/avantika';
BATCH.filename = fullfile(Datapath, SubId, strcat(SubId,'_conn_project.mat'));
% Batch Setup
BATCH.Setup.nsessions = 1;
BATCH.Setup.RT = 1;
BATCH.Setup.acquisitiontype=1;
BATCH.Setup.functionals{1}{1} = fullfile(Datapath, SubId, strcat(SubId,'_',Runs,'.nii'));
BATCH.Setup.structurals{1} = fullfile(Datapath, SubId, strcat(SubId,'_T1.nii'));
BATCH.Setup.outputfiles=[1,1,0];
% Batch Preprocessing
BATCH.Setup.preprocessing.art_thresholds(1)= 9;
BATCH.Setup.preprocessing.art_thresholds(2)= 4;
BATCH.Setup.preprocessing.template_structural = '/work/nl3wanglab/avantika/nihpd_sym_04.5-08.5_t1w.nii';
BATCH.Setup.preprocessing.template_functional = '/work/nl3wanglab/avantika/nihpd_sym_04.5-08.5_t1w.nii';
%BATCH.Setup.preprocessing.tpm_ngaus = [2 2 2 4];
BATCH.Setup.preprocessing.voxelsize_anat = 1;
BATCH.Setup.preprocessing.voxelsize_func = 2.5;
BATCH.Setup.preprocessing.boundingbox = [-90,-126,-72;90,90,108];
BATCH.Setup.preprocessing.FWHM = 8;
BATCH.Setup.preprocessing.coregtomean = 1;
% Direct Normalization
BATCH.Setup.preprocessing.steps = {'functional_realign&unwarp', 'functional_center','functional_art','functional_segment&normalize_direct','structural_center','structural_segment&normalize','functional_smooth'};
conn_batch(BATCH);
And the error we are encountering is as follows:
>> conn_batch(BATCH);
Error using fprintf
Invalid file identifier. Use fopen to generate a valid file identifier.
Error using fprintf
Invalid file identifier. Use fopen to generate a valid file identifier.
Error in conn_disp (line 162)
for n=1:numel(str), fprintf(fh,'%s\n',str{n}); end
for n=1:numel(str), fprintf(fh,'%s\n',str{n}); end
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']);
conn_setup_preproc(varargin{:});
case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']);
conn_setup_preproc(varargin{:});
Error in conn_batch (line 1099)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
Threaded View
| Title | Author | Date |
|---|---|---|
| Carrie Brown | May 24, 2019 | |
| Alfonso Nieto-Castanon | May 25, 2019 | |
| Lachlan Strike | Aug 21, 2019 | |
| Alfonso Nieto-Castanon | Aug 21, 2019 | |
| Carrie Brown | May 29, 2019 | |