Failed slicetiming correction

Hi,

I performed fMRIPrep on a subject and received the following error:

3dTshift -ignore 3 -prefix sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-5_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s -tzero 0.967 /work/fmriprep_23_1_wf/single_subject_M2ID14087_wf/func_preproc_ses_1_task_EmotionalReactivityAndRecovery_run_5_wf/bold_stc_wf/slice_timing_correction/sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-5_bold.nii.gz
Stdout:

Stderr:
	++ 3dTshift: AFNI version=AFNI_23.2.02 (Jul 28 2023) [64-bit]
	e[7m** FATAL ERROR:e[0m tpattern file slice_timing.1D has 30 values but have 97 slices
	** Program compile date = Jul 28 2023

I’ve noted a previous post that had the same issue (Fmriprep slice timing issue - #2 by effigies), but I don’t feel it can be solved in the same way. This error has occurred for all functional runs, here is fslhd performed on one of the functional inputs:

filename	sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-1_bold.nii.gz

sizeof_hdr	348
data_type	INT16
dim0		4
dim1		64
dim2		64
dim3		30
dim4		265
dim5		1
dim6		1
dim7		1
vox_units	mm
time_units	s
datatype	4
nbyper		2
bitpix		16
pixdim0		1.000000
pixdim1		3.750000
pixdim2		3.750000
pixdim3		5.000000
pixdim4		2.000000
pixdim5		0.000000
pixdim6		0.000000
pixdim7		0.000000
vox_offset	352
cal_max		0.000000
cal_min		0.000000
scl_slope	0.000000
scl_inter	0.000000
phase_dim	0
freq_dim	0
slice_dim	3
slice_name	alternating_increasing
slice_code	3
slice_start	0
slice_end	29
slice_duration	0.066667
toffset		0.000000
intent		Unknown
intent_code	0
intent_name	
intent_p1	0.000000
intent_p2	0.000000
intent_p3	0.000000
qform_name	Scanner Anat
qform_code	1
qto_xyz:1	0.000000 0.000000 5.000000 -76.599998 
qto_xyz:2	-3.750000 0.000000 0.000000 119.885002 
qto_xyz:3	0.000000 -3.750000 0.000000 136.854996 
qto_xyz:4	0.000000 0.000000 0.000000 1.000000 
qform_xorient	Anterior-to-Posterior
qform_yorient	Superior-to-Inferior
qform_zorient	Left-to-Right
sform_name	Scanner Anat
sform_code	1
sto_xyz:1	-0.000000 -0.000000 5.000000 -76.599998 
sto_xyz:2	-3.750000 -0.000000 -0.000000 119.885002 
sto_xyz:3	0.000000 -3.750000 0.000000 136.854996 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 
sform_xorient	Anterior-to-Posterior
sform_yorient	Superior-to-Inferior
sform_zorient	Left-to-Right
file_type	NIFTI-1+
file_code	1
descrip		
aux_file	

fslhd doesn’t work on /storage/gold/cinn/2021/midus/tmp/fmriprep_23_1_wf/single_subject_M2ID14087_wf/func_preproc_ses_1_task_EmotionalReactivityAndRecovery_run_1_wf/bold_stc_wf/slice_timing_correction.nii.gz (per previous post) due to being a “broken link”.

It’s worth noting I have previously, and successfully, performed fMRIPrep on this subject using version 20.2.6 (now using 23.1.4).

Any help would be greatly appreciated!

What’s the fslhd on /work/fmriprep_23_1_wf/single_subject_M2ID14087_wf/func_preproc_ses_1_task_EmotionalReactivityAndRecovery_run_5_wf/bold_stc_wf/slice_timing_correction/sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-5_bold.nii.gz?

I don’t have that file path, the closest I get is the one specified in my initial post (apologies, formatting of the post didn’t make it very clear). Here it is again, however, for run 5 (all runs are the same though):

storage/gold/cinn/2021/midus/tmp/fmriprep_23_1_wf/single_subject_M2ID14087_wf/func_preproc_ses_1_task_EmotionalReactivityAndRecovery_run_5_wf/bold_stc_wf/slice_timing_correction/sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-5_bold.nii.gz (which is a broken link). This is a list of all files within the slice_timing_correction directory:

command.txt
_inputs.pklz
_node.pklz
_report
result_slice_timing_correction.pklz
slice_timing.1D
sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-5_bold.nii.gz

What is the link to?

(Also, please escape your code and terminal outputs. I’m not sure why Neurostars doesn’t have a quick-start for Discourse, but here’s one for Python’s: Python Discourse Quick Start - Welcome to Discourse! - Discussions on Python.org)

That’s the “Type” of the file, it doesn’t do anything. Here is a screenshot of my directory:

The link will have a target. What do you get if you run readlink on it?

I get the following:

/data/sub-M2ID14087/ses-1/func/sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-5_bold.nii.gz

Okay, so that’s just a link to your raw data file. What’s the fslhd of sub-M2ID14087/ses-1/func/sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-5_bold.nii.gz?

filename sub-M2ID14087_ses-1_task-EmotionalReactivityAndRecovery_run-5_bold.nii.gz

sizeof_hdr 348
data_type INT16
dim0 4
dim1 97
dim2 115
dim3 97
dim4 265
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 1.000000
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 2.000000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
vox_offset 352
cal_max 0.000000
cal_min 0.000000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
toffset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name MNI_152
qform_code 4
qto_xyz:1 2.000000 0.000000 0.000000 -96.500000
qto_xyz:2 0.000000 2.000000 0.000000 -132.500000
qto_xyz:3 0.000000 0.000000 2.000000 -78.500000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name MNI_152
sform_code 4
sto_xyz:1 2.000000 0.000000 0.000000 -96.500000
sto_xyz:2 0.000000 2.000000 0.000000 -132.500000
sto_xyz:3 0.000000 0.000000 2.000000 -78.500000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip 6.0.5:9e026117
aux_file

That seems to be the issue.