help > BATCH unrecognized option done.
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Mar 27, 2020 09:03 PM | Romke Hannema - McGill University
BATCH unrecognized option done.
To whom it may concern,
In my script to run a CONN analysis, I am trying to make it do a certain sequence of preprocessing steps, using the following script:
BATCH.Setup.preprocessing.steps={'functional_label_as_original','functional_realign&unwarp','functional_center', 'functional_art', 'functional_segment&normalize_indirect', 'functional_label_as_mnispace','structural_center', 'structural_segment&normalize', 'functional_smooth', 'functional_label_as_smoothed'};
BATCH.Setup.preprocessing.voxelsize_anat=0.8;
BATCH.Setup.preprocessing.voxelsize_func=2;
BATCH.Setup.preprocessing.fwhm=6;
BATCH.Setup.preprocessing.done=1;
BATCH.Setup.preprocessing.overwrite='No';
However, I continually keep getting the error:
Error using conn_setup_preproc (line 380)
unrecognized option done
Error in conn_process (line 27)
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{:});
Error in Batch_all_subjects (line 58)
conn_batch(BATCH);
Even if I replace the BATCH.Setup.preprocessing.steps with {'default_mni'}, I get the same error. This also happens if I add a preprocessing option that makes no sense, like {'bananas'}. This indicates to me that somehow, one of the options that I'm adding is being registered as nonexistent/invalid. This doesn't make much sense to me, as I've retrieved all these step names using 'help conn_batch'.
Any help/suggestions would be welcome and appreciated.
Kind regards,
Romke Hannema
In my script to run a CONN analysis, I am trying to make it do a certain sequence of preprocessing steps, using the following script:
BATCH.Setup.preprocessing.steps={'functional_label_as_original','functional_realign&unwarp','functional_center', 'functional_art', 'functional_segment&normalize_indirect', 'functional_label_as_mnispace','structural_center', 'structural_segment&normalize', 'functional_smooth', 'functional_label_as_smoothed'};
BATCH.Setup.preprocessing.voxelsize_anat=0.8;
BATCH.Setup.preprocessing.voxelsize_func=2;
BATCH.Setup.preprocessing.fwhm=6;
BATCH.Setup.preprocessing.done=1;
BATCH.Setup.preprocessing.overwrite='No';
However, I continually keep getting the error:
Error using conn_setup_preproc (line 380)
unrecognized option done
Error in conn_process (line 27)
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{:});
Error in Batch_all_subjects (line 58)
conn_batch(BATCH);
Even if I replace the BATCH.Setup.preprocessing.steps with {'default_mni'}, I get the same error. This also happens if I add a preprocessing option that makes no sense, like {'bananas'}. This indicates to me that somehow, one of the options that I'm adding is being registered as nonexistent/invalid. This doesn't make much sense to me, as I've retrieved all these step names using 'help conn_batch'.
Any help/suggestions would be welcome and appreciated.
Kind regards,
Romke Hannema
Mar 28, 2020 12:03 PM | Alfonso Nieto-Castanon - Boston University
RE: BATCH unrecognized option done.
Hi Romke
Please try removing the lines
BATCH.Setup.preprocessing.done=1;
BATCH.Setup.preprocessing.overwrite='No';
since there is really no field "done" or "overwrite" within Setup.preprocessing (see "doc conn_batch" for more details; https://web.conn-toolbox.org/resources/c...)
Best
Alfonso
Originally posted by Romke Hannema:
Please try removing the lines
BATCH.Setup.preprocessing.done=1;
BATCH.Setup.preprocessing.overwrite='No';
since there is really no field "done" or "overwrite" within Setup.preprocessing (see "doc conn_batch" for more details; https://web.conn-toolbox.org/resources/c...)
Best
Alfonso
Originally posted by Romke Hannema:
To whom it may concern,
In my script to run a CONN analysis, I am trying to make it do a certain sequence of preprocessing steps, using the following script:
BATCH.Setup.preprocessing.steps={'functional_label_as_original','functional_realign&unwarp','functional_center', 'functional_art', 'functional_segment&normalize_indirect', 'functional_label_as_mnispace','structural_center', 'structural_segment&normalize', 'functional_smooth', 'functional_label_as_smoothed'};
BATCH.Setup.preprocessing.voxelsize_anat=0.8;
BATCH.Setup.preprocessing.voxelsize_func=2;
BATCH.Setup.preprocessing.fwhm=6;
BATCH.Setup.preprocessing.done=1;
BATCH.Setup.preprocessing.overwrite='No';
However, I continually keep getting the error:
Error using conn_setup_preproc (line 380)
unrecognized option done
Error in conn_process (line 27)
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{:});
Error in Batch_all_subjects (line 58)
conn_batch(BATCH);
Even if I replace the BATCH.Setup.preprocessing.steps with {'default_mni'}, I get the same error. This also happens if I add a preprocessing option that makes no sense, like {'bananas'}. This indicates to me that somehow, one of the options that I'm adding is being registered as nonexistent/invalid. This doesn't make much sense to me, as I've retrieved all these step names using 'help conn_batch'.
Any help/suggestions would be welcome and appreciated.
Kind regards,
Romke Hannema
In my script to run a CONN analysis, I am trying to make it do a certain sequence of preprocessing steps, using the following script:
BATCH.Setup.preprocessing.steps={'functional_label_as_original','functional_realign&unwarp','functional_center', 'functional_art', 'functional_segment&normalize_indirect', 'functional_label_as_mnispace','structural_center', 'structural_segment&normalize', 'functional_smooth', 'functional_label_as_smoothed'};
BATCH.Setup.preprocessing.voxelsize_anat=0.8;
BATCH.Setup.preprocessing.voxelsize_func=2;
BATCH.Setup.preprocessing.fwhm=6;
BATCH.Setup.preprocessing.done=1;
BATCH.Setup.preprocessing.overwrite='No';
However, I continually keep getting the error:
Error using conn_setup_preproc (line 380)
unrecognized option done
Error in conn_process (line 27)
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{:});
Error in Batch_all_subjects (line 58)
conn_batch(BATCH);
Even if I replace the BATCH.Setup.preprocessing.steps with {'default_mni'}, I get the same error. This also happens if I add a preprocessing option that makes no sense, like {'bananas'}. This indicates to me that somehow, one of the options that I'm adding is being registered as nonexistent/invalid. This doesn't make much sense to me, as I've retrieved all these step names using 'help conn_batch'.
Any help/suggestions would be welcome and appreciated.
Kind regards,
Romke Hannema