Hi all,

I am preprocessing some resting-state fMRI data, and I keep getting an error right after the SPM Batch module "Realign: Estimate and Reslice" saying "Error using harvest (line 47). Dependencies resolved, but not suitable for this item".

I can understand there's something wrong in the process of taking the output of Realignment to the next step (Slice Timing), but I don't understand why. I checked the quality of the data and they seem fine, the dependencies are correct in the batch, and I am using the default parameters as indicated in the SPM manual (SPM12).

Anyone has had this problem before?

Many thanks

Best,
Sara

> Hi Sara
I don’t have enough information about your data, but you have to check your rfmri information with SPM defaults. They are not always works for all images.
Best
Mehrnaz

Dear Mehrnaz,

I am dealing with 20 minutes-long resting-state fmri data collected during 3 different tDCS stimulation conditions (sham, anodal, cathodal). Data were collected with a Philips Achieva scanner.

Here below is the beginning of my batch preprocessing pipeline (Realign - Estimate and Reslice, and Slice Timing):

matlabbatch{1}.cfg_basicio.file_dir.dir_ops.cfg_cd.dir = '';
matlabbatch{2}.spm.spatial.realign.estwrite.data = {''};
matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;
matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.sep = 4;
matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;
matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.rtm = 1;
matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.interp = 2;
matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.weight = '';
matlabbatch{2}.spm.spatial.realign.estwrite.roptions.which = [2 1];
matlabbatch{2}.spm.spatial.realign.estwrite.roptions.interp = 4;
matlabbatch{2}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];
matlabbatch{2}.spm.spatial.realign.estwrite.roptions.mask = 1;
matlabbatch{2}.spm.spatial.realign.estwrite.roptions.prefix = 'r';

matlabbatch{3}.spm.temporal.st.scans{1}(1) = cfg_dep('Realign: Estimate & Reslice: Resliced Images (Sess 1)', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','rfiles'));
matlabbatch{3}.spm.temporal.st.nslices = 34;
matlabbatch{3}.spm.temporal.st.tr = 2;
matlabbatch{3}.spm.temporal.st.ta = 1.94117647058824;
matlabbatch{3}.spm.temporal.st.so = [1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34];
matlabbatch{3}.spm.temporal.st.refslice = 1;
matlabbatch{3}.spm.temporal.st.prefix = 'a';


Attached you can find the script I'm using for calling inputs and job file (I'm trying with just one subject and the three tdcs conditions).
The error that I get after the realignment step is the following:


Done 'Realign: Estimate & Reslice'
Item 'Session', field 'val': Number of matching files (1) less than required (2).
Error using harvest (line 47)
Dependencies resolved, but not suitable for this item.
In item Session:
Dependency 1: Realign: Estimate & Reslice: Resliced Images (Sess 1)
(out.sess(1).rfiles)
'/projects/pbic1036/sara/bids_m1_data/derivatives/preprocessing/sub-0…'

Error in harvest (line 62)
Error in harvest (line 49)
Error in harvest (line 51)
Error in cfg_util>local_runcj (line 1723)
Error in cfg_util (line 959)
Error in spm_jobman>fill_run_job (line 458)
Error in spm_jobman (line 247)
Error in preprocessing_lets_try (line 29)


Any idea of what could be causing this error?
Many thanks

Best,
Sara