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.
