Hi Nicole, Group,
I am having the same problem that you posted on July 7th of 2009 (pasted below). I do not see a posted response/solution to your inquiry and am wondering if you ever worked the problem out. This is my first time using the FSL LISTSERV, I hope I am inquiring properly.
Here is a part of the error (same as yours below):
/usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_thresh
/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
/usr/local/fsl/bin/susan prefiltered_func_data_thresh 19956.6782228 2.12314225053 3 1 1 mean_func 19956.6782228 prefiltered_func_data_smooth
/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth
** ERROR (nifti_image_read): failed to find header file for 'prefiltered_func_data_smooth'
** ERROR: nifti_image_open(prefiltered_func_data_smooth): bad header info
Error: failed to open file prefiltered_func_data_smooth
Cannot open volume prefiltered_func_data_smooth for reading!
Thanks in advance,
Derek
Subject:
SUSAN in FEAT w/ single-slice data
From:
Nicole Pelot <[log in to unmask]>
Reply-To:
FSL - FMRIB's Software Library <[log in to unmask]>
Date:
Tue, 7 Jul 2009 14:50:59 +0100
Hi,
I'm processing some single-slice data with FEAT, as I have done before, but
I believe that the FSL version we use has been updated since the last time.
It now runs into an error in Pre-stats, which clearly prevents the rest of
the analysis from running:
*********
/usr/local/fsl/bin/fslmaths
/home/nicolep/Nicole/matlab/LinearVsInterleaved/0630_int_g0_1sl
prefiltered_func_data -odt float
Total original volumes = 140
/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 70 1
/usr/local/fsl/bin/fslstats prefiltered_func_data -p 2 -p 98
0.000000 14503.965820
/usr/local/fsl/bin/fslmaths prefiltered_func_data -thr 1450.396582 -Tmin
-bin mask -odt char
/usr/local/fsl/bin/fslstats prefiltered_func_data -k mask -p 50
0.000000
/usr/local/fsl/bin/fslmaths mask -dilF mask
/usr/local/fsl/bin/fslmaths prefiltered_func_data -mas mask
prefiltered_func_data_thresh
/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
/usr/local/fsl/bin/susan prefiltered_func_data_thresh 0.0 2.54777070064 3 1
1 mean_func 0.0 prefiltered_func_data_smooth
/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask
prefiltered_func_data_smooth
** ERROR (nifti_image_read): failed to find header file for
'prefiltered_func_data_smooth'
** ERROR: nifti_image_open(prefiltered_func_data_smooth): bad header info
Error: failed to open file prefiltered_func_data_smooth
Cannot open volume prefiltered_func_data_smooth for reading!
divide by zero
while executing
"expr $normmean / $median_intensity "
(procedure "feat5:proc_prestats" line 406)
invoked from within
"feat5:proc_prestats $session "
("-prestats" arm line 2)
invoked from within
"switch -- [ lindex $argv $argindex ] {
-I {
incr argindex 1
set session [ lindex $argv $argindex ]
}
-D {
incr argindex 1
set..."
("for" body line 2)
invoked from within
"for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr argindex 1
set ses..."
(file "/usr/local/fsl/bin/feat" line 137)
*********
I pulled up the log from an older analysis, as seen below.
*********
/usr/local/fsl/bin/fslmaths
/home/nicolep/Nicole/matlab/s_20090312_01/Analysis/0312_07_OneSliceMiddle
prefiltered_func_data
Total original volumes = 70
/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 35 1
/usr/local/fsl/bin/fslmaths prefiltered_func_data -thrp 10 -Tmin -bin mask
-odt char
/usr/local/fsl/bin/fslmaths prefiltered_func_data -mas mask
prefiltered_func_data
/usr/local/fsl/bin/fslmaths mask -kernel gauss 2.54777070064 -fmean
mask_weight -odt float
/usr/local/fsl/bin/fslmaths prefiltered_func_data -kernel gauss
2.54777070064 -fmean -div mask_weight -mas mask filtered_func_data -odt float
/usr/local/fsl/bin/fslmaths filtered_func_data -ing 10000 filtered_func_data
-odt float
/usr/local/fsl/bin/fslmaths filtered_func_data -bptf 20.0 -1
filtered_func_data -odt float
/usr/local/fsl/bin/fslhd -x filtered_func_data | sed 's/ dt = .*/ dt =
'5.6'/g' | /usr/local/fsl/bin/fslcreatehd - filtered_func_data
/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func
/bin/rm -rf prefiltered_func_data*
*********
The one significant difference between these analyses is that the new one
(with the error) uses perfusion subtraction, whereas the old one did not,
but I believe that the error is occurring before any perfusion subtraction
steps. In addition, I significantly changed the data processing prior to
running FEAT, so it is possible that something went wrong even before FEAT.
My best guess at the cause of the problem is that the call to "susan" for
spatial smoothing is 3D, whereas I would need it 2D. Is this correct? Is
there a way around it? Were my data even being smoothed beforehand, or did
it automatically bypass smoothing because the data were 2D?
Thanks for your help,
Nicole
P.S.: I can upload my data if need be.
