Hi Catherine,
Hi Maarten,There is indeed an error....failed to find the header file...does that mean there is a conversion problem when I converted the data from dicom to nii?
I copied the log below.../home/fsl/Desktop/fsl/bin/featregapply /media/fsl/DATA/IBMT78FSL/I7PRE/0002144/1_004_MoCoSeries_20110121_IBMT78FSLANALYSIS.ica
Error - registration has not been run for /media/fsl/DATA/IBMT78FSL/I7PRE/0002144/1_004_MoCoSeries_20110121_IBMT78FSLANALYSIS.ica
/home/fsl/Desktop/fsl/bin/fslmerge -t bg_image /media/fsl/DATA/IBMT78FSL/I7PRE/0001773/1_004_MoCoSeries_20110118/0001773_20110118_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/bg_image /media/fsl/DATA/IBMT78FSL/I7PRE/0001982/1_004_MoCoSeries_20110118/0001982_20110118_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/bg_image /media/fsl/DATA/IBMT78FSL/I7PRE/0002137/1_004_MoCoSeries_20110119/0002137_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/bg_image /media/fsl/DATA/IBMT78FSL/I7PRE/0002138/1_004_MoCoSeries_20110119/0002138_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/bg_image /media/fsl/DATA/IBMT78FSL/I7PRE/0002139/1_004_MoCoSeries_20110119/0002139_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/bg_image /media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/bg_image /media/fsl/DATA/IBMT78FSL/I7PRE/0002141/1_004_MoCoSeries_20110120/0002141_20110120_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/bg_image /media/fsl/DATA/IBMT78FSL/I7PRE/0002144/1_004_MoCoSeries_20110121_IBMT78FSLANALYSIS.ica/reg_standard/bg_image
** ERROR (nifti_image_read): failed to find header file for '/media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/bg_image'
** ERROR: nifti_image_open(/media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/bg_image): bad header info
ERROR: failed to open file /media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/bg_image
ERROR: Could not open image /media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/bg_image
Image Exception : #22 :: Failed to read volume /media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/bg_image
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float
** ERROR (nifti_image_read): failed to find header file for 'bg_image'
** ERROR: nifti_image_open(bg_image): bad header info
ERROR: failed to open file bg_image
Cannot open volume bg_image for reading!
/home/fsl/Desktop/fsl/bin/fslmerge -t mask /media/fsl/DATA/IBMT78FSL/I7PRE/0001773/1_004_MoCoSeries_20110118/0001773_20110118_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask /media/fsl/DATA/IBMT78FSL/I7PRE/0001982/1_004_MoCoSeries_20110118/0001982_20110118_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask /media/fsl/DATA/IBMT78FSL/I7PRE/0002137/1_004_MoCoSeries_20110119/0002137_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask /media/fsl/DATA/IBMT78FSL/I7PRE/0002138/1_004_MoCoSeries_20110119/0002138_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask /media/fsl/DATA/IBMT78FSL/I7PRE/0002139/1_004_MoCoSeries_20110119/0002139_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask /media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/mask /media/fsl/DATA/IBMT78FSL/I7PRE/0002141/1_004_MoCoSeries_20110120/0002141_20110120_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask /media/fsl/DATA/IBMT78FSL/I7PRE/0002144/1_004_MoCoSeries_20110121_IBMT78FSLANALYSIS.ica/reg_standard/mask
** ERROR (nifti_image_read): failed to find header file for '/media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/mask'
** ERROR: nifti_image_open(/media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/mask): bad header info
ERROR: failed to open file /media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/mask
ERROR: Could not open image /media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/mask
Image Exception : #22 :: Failed to read volume /media/fsl/DATA/IBMT78FSL/I7PRE/0002140/1_005_MoCoSeries_20110120_IBMT78FSLANALYSIS.ica/reg_standard/mask
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
mkdir -p inputreg
/home/fsl/Desktop/fsl/bin/fslmaths ../mask -mul 8 -Tmean masksum -odt short
** ERROR (nifti_image_read): failed to find header file for '../mask'
** ERROR: nifti_image_open(../mask): bad header info
ERROR: failed to open file ../mask
Cannot open volume ../mask for reading!
/home/fsl/Desktop/fsl/bin/fslmaths masksum -thr 8 -add masksum masksum
** ERROR (nifti_image_read): failed to find header file for 'masksum'
** ERROR: nifti_image_open(masksum): bad header info
ERROR: failed to open file masksum
Cannot open volume masksum for reading!
/home/fsl/Desktop/fsl/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 16 masksum_overlay
** ERROR (nifti_image_read): failed to find header file for '../bg_image'
** ERROR: nifti_image_open(../bg_image): bad header info
ERROR: failed to open file ../bg_image
ERROR: Could not open image ../bg_image
Image Exception : #22 :: Failed to read volume ../bg_image
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png
** ERROR (nifti_image_read): failed to find header file for 'masksum_overlay'
** ERROR: nifti_image_open(masksum_overlay): bad header info
ERROR: failed to open file masksum_overlay
ERROR: Could not open image masksum_overlay
Image Exception : #22 :: Failed to read volume masksum_overlay
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/fslmaths masksum -mul 0 maskunique
** ERROR (nifti_image_read): failed to find header file for 'masksum'
** ERROR: nifti_image_open(masksum): bad header info
ERROR: failed to open file masksum
Cannot open volume masksum for reading!
/home/fsl/Desktop/fsl/bin/fslmaths /media/fsl/DATA/IBMT78FSL/I7PRE/0001773/1_004_MoCoSeries_20110118/0001773_20110118_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for 'maskunique'
** ERROR: nifti_image_open(maskunique): bad header info
ERROR: failed to open file maskunique
ERROR: Could not open image maskunique
Image Exception : #22 :: Failed to read volume maskunique
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/fslmaths /media/fsl/DATA/IBMT78FSL/I7PRE/0001982/1_004_MoCoSeries_20110118/0001982_20110118_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for 'maskunique'
** ERROR: nifti_image_open(maskunique): bad header info
ERROR: failed to open file maskunique
ERROR: Could not open image maskunique
Image Exception : #22 :: Failed to read volume maskunique
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/fslmaths /media/fsl/DATA/IBMT78FSL/I7PRE/0002137/1_004_MoCoSeries_20110119/0002137_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for 'maskunique'
** ERROR: nifti_image_open(maskunique): bad header info
ERROR: failed to open file maskunique
ERROR: Could not open image maskunique
Image Exception : #22 :: Failed to read volume maskunique
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/fslmaths /media/fsl/DATA/IBMT78FSL/I7PRE/0002138/1_004_MoCoSeries_20110119/0002138_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for 'maskunique'
** ERROR: nifti_image_open(maskunique): bad header info
ERROR: failed to open file maskunique
ERROR: Could not open image maskunique
Image Exception : #22 :: Failed to read volume maskunique
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/fslmaths /media/fsl/DATA/IBMT78FSL/I7PRE/0002139/1_004_MoCoSeries_20110119/0002139_20110119_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for 'maskunique'
** ERROR: nifti_image_open(maskunique): bad header info
ERROR: failed to open file maskunique
ERROR: Could not open image maskunique
Image Exception : #22 :: Failed to read volume maskunique
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/fslmaths 0 -mul -1 -add 1 -mul 6 -add maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for '0'
** ERROR: nifti_image_open(0): bad header info
ERROR: failed to open file 0
Cannot open volume 0 for reading!
/home/fsl/Desktop/fsl/bin/fslmaths /media/fsl/DATA/IBMT78FSL/I7PRE/0002141/1_004_MoCoSeries_20110120/0002141_20110120_001_004_PACE_EPI_RESTING_1_MoCoSeries_IBMT78FSLANALYSIS.ica/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for 'maskunique'
** ERROR: nifti_image_open(maskunique): bad header info
ERROR: failed to open file maskunique
ERROR: Could not open image maskunique
Image Exception : #22 :: Failed to read volume maskunique
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/fslmaths 0 -mul -1 -add 1 -mul 8 -add maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for '0'
** ERROR: nifti_image_open(0): bad header info
ERROR: failed to open file 0
Cannot open volume 0 for reading!
/home/fsl/Desktop/fsl/bin/fslmaths masksum -thr 7 -uthr 7 -bin -mul maskunique maskunique
** ERROR (nifti_image_read): failed to find header file for 'masksum'
** ERROR: nifti_image_open(masksum): bad header info
ERROR: failed to open file masksum
Cannot open volume masksum for reading!
/home/fsl/Desktop/fsl/bin/overlay 0 0 ../bg_image -a maskunique 0.9 8 maskunique_overlay
** ERROR (nifti_image_read): failed to find header file for '../bg_image'
** ERROR: nifti_image_open(../bg_image): bad header info
ERROR: failed to open file ../bg_image
ERROR: Could not open image ../bg_image
Image Exception : #22 :: Failed to read volume ../bg_image
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/Desktop/fsl/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png
** ERROR (nifti_image_read): failed to find header file for 'maskunique_overlay'
** ERROR: nifti_image_open(maskunique_overlay): bad header info
ERROR: failed to open file maskunique_overlay
ERROR: Could not open image maskunique_overlay
Image Exception : #22 :: Failed to read volume maskunique_overlay
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/bin/cp /home/fsl/Desktop/fsl/etc/luts/ramp.gif .ramp.gif
/home/fsl/Desktop/fsl/bin/fslmaths mask -Tmin -bin mask -odt char
** ERROR (nifti_image_read): failed to find header file for 'mask'
** ERROR: nifti_image_open(mask): bad header info
ERROR: failed to open file mask
Cannot open volume mask for reading!
/home/fsl/Desktop/fsl/bin/melodic -i .filelist -o groupmelodic.ica -v --nobet --bgthreshold=10 --tr=2.0 --report --guireport=../../report.html --bgimage=bg_image -d 0 --mmthresh=0.5 -a tica
Melodic Version 3.10
Melodic results will be in groupmelodic.ica
Create mask ... done
** ERROR (nifti_image_read): failed to find header file for 'bg_image'
** ERROR: nifti_image_open(bg_image): bad header info
ERROR: failed to open file bg_image
ERROR: Could not open image bg_image
Image Exception : #22 :: Failed to read volume bg_image
An exception has been thrown
Failed to read volume bg_imageTrace: read_volumeROI.
From: Maarten Mennes <[log in to unmask]>
To: [log in to unmask]
Sent: Friday, July 13, 2012 6:35 AM
Subject: Re: [FSL] Melodic post-stats results not shown
Hi Catherine,Are you looking at: report/00index.html? If you go into your melodic ouput folder is there a melodic_IC.nii.gz file? In the 'report' folder can you see .png and .html files for the components (e.g., IC_8.html)What does the Log say (log.txt), did it complete without errors?MaartenOn Fri, Jul 13, 2012 at 2:37 AM, Catherine Tang <[log in to unmask]> wrote:
Dear All,
I encountered a problem when I performed a multisubject ICA analysis in MELODIC.
From what I understand, I do not have to set up timeseries model, contrast,etc. for the analysis?
What I did was:
set up the data,pre-stats,reg,stats,and post stats tabs normally, and press GO.
It popped up a web page that has the following links on it:
Higher-Level MELODIC Report
/media/fsl/DATA/IBMT78FSLANALYSIS.gica
Started at Fri Jul 13 01:35:18 BST 2012 STILL RUNNING.
Inputs - Registration summary - MELODIC output - Log
However, when the analysis is done, it only showed the pre-stats and registration results...it did not generate the ICA maps..
Did I make some mistakes?
Thanks,
Catherine
--
Maarten Mennes, Ph.D.
Post-Doctoral Researcher
Donders Institute for Brain, Cognition and Behaviour
Dept. of Cognitive Neuroscience
Radboud University Nijmegen Medical Centre
Nijmegen
The Netherlands