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Hey Steve,
> Hi - the image dimensions of these files don’t match the design.fsf
> or the log files you sent before.
> Make sure that you are running this from the GUI, and selecting all
> inputs datasets in an up to date way in the GUI.
I didn't send the right design.fsf, but the errors and the settings
are the same for every of the send files. I didn't change the number
of volumes against the automatic detection nor did Melodic set a wrong
number.
> Also - some of these datasets are large - so make sure that you have
> plenty of RAM/swap for this.
The Ram/swap also doesn't matter: I did a NifTi out of only 100 Dicom
(instead of 1570)
volumes and I got the same error messages (that the design.fsf I sent).
Sorry for bothering, but I didn't change the usage behaviour with
Melodic. I tried a lot before considering to mail. I also followed the
instructions on the Feat FAQ section for debugging this kind of error.
I have attached the easiest example, and this time with everything needed.
I also searched for differences and I found a small one: the
example_func2highres.png
is missing in those cases where things went wrong comparing the "reg"
sub-directories.
Translation help:
/bin/rm: Entfernen von „example_func2highres1.png“ nicht möglich:
Datei oder Verzeichnis nicht gefunden
/bin/rm: Removing of „example_func2highres1.png“ not possible:
File or directory not found
Thanks once again and good night!
Matthias
# FEAT version number
set fmri(version) 3.14
# Are we in MELODIC?
set fmri(inmelodic) 1
# Analysis level
# 1 : First-level analysis
# 2 : Higher-level analysis
set fmri(level) 1
# Which stages to run
# 0 : No first-level analysis (registration and/or group stats only)
# 7 : Full first-level analysis
# 1 : Pre-Stats
# 3 : Pre-Stats + Stats
# 2 : Stats
# 6 : Stats + Post-stats
# 4 : Post-stats
set fmri(analysis) 7
# Use relative filenames
set fmri(relative_yn) 0
# Balloon help
set fmri(help_yn) 1
# Run Featwatcher
set fmri(featwatcher_yn) 0
# Cleanup first-level standard-space images
set fmri(sscleanup_yn) 0
# Output directory
set fmri(outputdir) "/media/data/Messdaten/Z2-TMS/100001/Pare/tr1286"
# TR(s)
set fmri(tr) 1.286000
# Total volumes
set fmri(npts) 455
# Delete volumes
set fmri(ndelete) 0
# Perfusion tag/control order
set fmri(tagfirst) 1
# Number of first-level analyses
set fmri(multiple) 1
# Higher-level input type
# 1 : Inputs are lower-level FEAT directories
# 2 : Inputs are cope images from FEAT directories
set fmri(inputtype) 1
# Carry out pre-stats processing?
set fmri(filtering_yn) 1
# Brain/background threshold, %
set fmri(brain_thresh) 10
# Critical z for design efficiency calculation
set fmri(critical_z) 5.3
# Noise level
set fmri(noise) 0.66
# Noise AR(1)
set fmri(noisear) 0.34
# Post-stats-only directory copying
# 0 : Overwrite original post-stats results
# 1 : Copy original FEAT directory for new Contrasts, Thresholding, Rendering
set fmri(newdir_yn) 0
# Motion correction
# 0 : None
# 1 : MCFLIRT
set fmri(mc) 1
# Spin-history (currently obsolete)
set fmri(sh_yn) 0
# B0 fieldmap unwarping?
set fmri(regunwarp_yn) 0
# EPI dwell time (ms)
set fmri(dwell) 0.7
# EPI TE (ms)
set fmri(te) 35
# % Signal loss threshold
set fmri(signallossthresh) 10
# Unwarp direction
set fmri(unwarp_dir) y-
# Slice timing correction
# 0 : None
# 1 : Regular up (0, 1, 2, 3, ...)
# 2 : Regular down
# 3 : Use slice order file
# 4 : Use slice timings file
# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
set fmri(st) 0
# Slice timings file
set fmri(st_file) ""
# BET brain extraction
set fmri(bet_yn) 1
# Spatial smoothing FWHM (mm)
set fmri(smooth) 5
# Intensity normalization
set fmri(norm_yn) 0
# Perfusion subtraction
set fmri(perfsub_yn) 0
# Highpass temporal filtering
set fmri(temphp_yn) 1
# Lowpass temporal filtering
set fmri(templp_yn) 0
# MELODIC ICA data exploration
set fmri(melodic_yn) 0
# Carry out main stats?
set fmri(stats_yn) 1
# Carry out prewhitening?
set fmri(prewhiten_yn) 1
# Add motion parameters to model
# 0 : No
# 1 : Yes
set fmri(motionevs) 0
set fmri(motionevsbeta) ""
set fmri(scriptevsbeta) ""
# Robust outlier detection in FLAME?
set fmri(robust_yn) 0
# Higher-level modelling
# 3 : Fixed effects
# 0 : Mixed Effects: Simple OLS
# 2 : Mixed Effects: FLAME 1
# 1 : Mixed Effects: FLAME 1+2
set fmri(mixed_yn) 2
# Number of EVs
set fmri(evs_orig) 1
set fmri(evs_real) 1
set fmri(evs_vox) 0
# Number of contrasts
set fmri(ncon_orig) 1
set fmri(ncon_real) 1
# Number of F-tests
set fmri(nftests_orig) 0
set fmri(nftests_real) 0
# Add constant column to design matrix? (obsolete)
set fmri(constcol) 0
# Carry out post-stats steps?
set fmri(poststats_yn) 1
# Pre-threshold masking?
set fmri(threshmask) ""
# Thresholding
# 0 : None
# 1 : Uncorrected
# 2 : Voxel
# 3 : Cluster
set fmri(thresh) 3
# P threshold
set fmri(prob_thresh) 0.05
# Z threshold
set fmri(z_thresh) 2.3
# Z min/max for colour rendering
# 0 : Use actual Z min/max
# 1 : Use preset Z min/max
set fmri(zdisplay) 0
# Z min in colour rendering
set fmri(zmin) 2
# Z max in colour rendering
set fmri(zmax) 8
# Colour rendering type
# 0 : Solid blobs
# 1 : Transparent blobs
set fmri(rendertype) 1
# Background image for higher-level stats overlays
# 1 : Mean highres
# 2 : First highres
# 3 : Mean functional
# 4 : First functional
# 5 : Standard space template
set fmri(bgimage) 1
# Create time series plots
set fmri(tsplot_yn) 1
# Registration?
set fmri(reg_yn) 1
# Registration to initial structural
set fmri(reginitial_highres_yn) 0
# Search space for registration to initial structural
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(reginitial_highres_search) 90
# Degrees of Freedom for registration to initial structural
set fmri(reginitial_highres_dof) 3
# Registration to main structural
set fmri(reghighres_yn) 1
# Search space for registration to main structural
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(reghighres_search) 90
# Degrees of Freedom for registration to main structural
set fmri(reghighres_dof) BBR
# Registration to standard image?
set fmri(regstandard_yn) 1
# Use alternate reference images?
set fmri(alternateReference_yn) 0
# Standard image
set fmri(regstandard) "/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain"
# Search space for registration to standard space
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(regstandard_search) 90
# Degrees of Freedom for registration to standard space
set fmri(regstandard_dof) 12
# Do nonlinear registration from structural to standard space?
set fmri(regstandard_nonlinear_yn) 1
# Control nonlinear warp field resolution
set fmri(regstandard_nonlinear_warpres) 10
# High pass filter cutoff
set fmri(paradigm_hp) 100
# Total voxels
set fmri(totalVoxels) 365281280
# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 0
# 4D AVW data or FEAT directory (1)
set feat_files(1) "/media/data/Messdaten/Z2-TMS/100001/Pare/s9-MEPI2mmTE262TR1286"
# Add confound EVs text file
set fmri(confoundevs) 0
# Subject's structural image for analysis 1
set highres_files(1) "/media/data/Messdaten/Z2-TMS/100001/T1/coBet0.4_brain"
# Resampling resolution
set fmri(regstandard_res) 0
# Variance-normalise timecourses
set fmri(varnorm) 1
# Automatic dimensionality estimation
set fmri(dim_yn) 1
# Output components
set fmri(dim) 1
# 1 : Single-session ICA
# 2 : Multi-session temporal concatenation
# 3 : Multi-session tensor TICA
set fmri(icaopt) 1
# Threshold IC maps
set fmri(thresh_yn) 1
# Mixture model threshold
set fmri(mmthresh) 0.5
# Output full stats folder
set fmri(ostats) 0
# Timeseries and subject models
set fmri(ts_model_mat) ""
set fmri(ts_model_con) ""
set fmri(subject_model_mat) ""
set fmri(subject_model_con) ""
##########################################################
# Now options that don't appear in the GUI
# Alternative (to BETting) mask image
set fmri(alternative_mask) ""
# Initial structural space registration initialisation transform
set fmri(init_initial_highres) ""
# Structural space registration initialisation transform
set fmri(init_highres) ""
# Standard space registration initialisation transform
set fmri(init_standard) ""
# For full FEAT analysis: overwrite existing .feat output dir?
set fmri(overwrite_yn) 0
filename s9-MEPI2mmTE262TR1286.nii.gz
sizeof_hdr 348
data_type INT16
dim0 4
dim1 112
dim2 112
dim3 64
dim4 455
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.286000
pixdim5 1.000000
pixdim6 0.689998
pixdim7 62413.121094
vox_offset 352
cal_max 0.0000
cal_min 0.0000
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 77.279755
time_offset 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 -1.996253 -0.041119 0.115255 120.379913
qto_xyz:2 -0.061528 1.965551 -0.364449 -79.195549
qto_xyz:3 0.105777 0.367311 1.963134 -46.276245
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.996253 -0.041118 0.115255 120.379913
sto_xyz:2 -0.061528 1.965551 -0.364449 -79.195549
sto_xyz:3 0.105777 0.367311 1.963134 -46.276245
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
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