Hi,
I really don't understand what is happening here as it is not a problem at this end.
I notice that you do not have $FSLDIR/bin in your path, although you do have
/usr/lib/fsl/4.1 instead. Can you do "which sienax" at the command line to
check that you are actually picking up the right version of FSL?
All the best,
Mark
On 10 Jan 2011, at 19:24, Graeme Schwindt wrote:
> Hi Mark -
>
> The usage message pops out immediately with no processing. If I write something nonsensical in the double quotes I get true errors, e.g.:
>
> sienax test_sienax.img -B "nonsense"
>
> ** ERROR (nifti_image_read): failed to find header file for 'I_brain'
> ** ERROR: nifti_image_open(I_brain): bad header info
> Error: failed to open file I_brain
> ERROR: Could not open image I_brain
> Image Exception : #22 :: Failed to read volume I_brain
> ** ERROR (nifti_image_read): failed to find header file for 'I_brain'
> ** ERROR: nifti_image_open(I_brain): bad header info
> Error: failed to open file I_brain
>
> ... etc etc
>
>
> We are running 4.1.6, here is the fslerrorreport
>
> ######################################################################
> #### MACHINE INFORMATION
> ######################################################################
>
> Uname:
> Linux
>
> df:
> Filesystem 1K-blocks Used Available Use% Mounted on
> synapse:/nt 6670602176 5242573312 1089181792 83% /net/synapse/nt
>
> quota:
>
> Memory and Swap info:
> MemTotal: 12326784 kB
> MemFree: 664168 kB
> Buffers: 3384 kB
> Cached: 116104 kB
> SwapCached: 16584 kB
> Active: 9723276 kB
> Inactive: 1528804 kB
> Active(anon): 9663664 kB
> Inactive(anon): 1469020 kB
> Active(file): 59612 kB
> Inactive(file): 59784 kB
> Unevictable: 0 kB
> Mlocked: 0 kB
> SwapTotal: 1952760 kB
> SwapFree: 1526680 kB
> Dirty: 4 kB
> Writeback: 0 kB
> AnonPages: 11119928 kB
> Mapped: 16632 kB
> Shmem: 92 kB
> Slab: 94880 kB
> SReclaimable: 69184 kB
> SUnreclaim: 25696 kB
> KernelStack: 3752 kB
> PageTables: 41840 kB
> NFS_Unstable: 0 kB
> Bounce: 0 kB
> WritebackTmp: 0 kB
> CommitLimit: 8116152 kB
> Committed_AS: 9577960 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed: 310012 kB
> VmallocChunk: 34359424284 kB
> HardwareCorrupted: 0 kB
> HugePages_Total: 0
> HugePages_Free: 0
> HugePages_Rsvd: 0
> HugePages_Surp: 0
> Hugepagesize: 2048 kB
> DirectMap4k: 7488 kB
> DirectMap2M: 12570624 kB
>
> ######################################################################
> #### ENVIRONMENT INFORMATION
> ######################################################################
> FSLDIR=/usr/share/fsl/4.1
> FSLMULTIFILEQUIT=TRUE
> FSLTCLSH=/usr/bin/tclsh
> FSLMACHINELIST=
> FSLOUTPUTTYPE=NIFTI_GZ
> FSLBROWSER=/etc/alternatives/x-www-browser
> FSLREMOTECALL=
> FSLWISH=/usr/bin/wish
> FSLLOCKDIR=
>
> LD_LIBRARY_PATH=/usr/lib/fsl/4.1
> DCMDICTPATH=/usr/share/dcmtk/dicom.dic
> PATH=/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/opt/AIR5
> .2.6/bin:/opt/BIR/bin:/opt/irtk:/opt/ge:/opt/debabeler:/opt/pipeline:/opt/mni/bin:/net/synapse/nt/shared/pub/freezer/LesionTraining/AutoLesion:/opt/sb/szilag
> yi/cross-platform/bin:/usr/lib/afni/bin/:/opt/freesurfer/bin:/usr/lib/fsl/4.1:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/opt/AI
> R5.2.6/bin:/opt/BIR/bin:/opt/ge:/opt/debabeler:/opt/pipeline:/opt/mni/bin:/net/synapse/nt/shared/pub/freezer/LesionTraining/AutoLesion:/opt/sb/szilagyi/cross
> -platform/bin
> CDPATH=
> MNI_DATAPATH=/opt/freesurfer/mni/data
> LD_LIBRARY_PATH=/usr/lib/fsl/4.1
>
> ######################################################################
> #### DIRECTORY INFORMATION
> ######################################################################
>
> PWD:
> /net/synapse/nt/adgroup/gschwindt/test_SIENAX
>
> total 23848
> drwxr-xr-x 2 gschwind agesb 4096 2011-01-10 14:16 .
> drwxr-xr-x 15 gschwind agesb 4096 2011-01-10 14:15 ..
> -rw-r--r-- 1 gschwind agesb 0 2011-01-10 14:16 errorreport.txt
> -rwxr-x--- 1 gschwind agesb 348 2011-01-10 12:32 test_sienax.hdr
> -rwxr-x--- 1 gschwind agesb 24379392 2011-01-10 12:32 test_sienax.img
>
> ######################################################################
> #### IMAGE INFORMATION
> ######################################################################
>
> Byte swapping
> filename test_sienax.img
>
> sizeof_hdr 348
> data_type
> db_name
> extents 0
> session_error 0
> regular r
> hkey_un0
> dim0 4
> dim1 256
> dim2 256
> dim3 186
> dim4 1
> dim5 0
> dim6 0
> dim7 0
> vox_units
> cal_units
> unused1 0
> datatype 4
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 0.8593999743
> pixdim2 0.8593999743
> pixdim3 1.0000000000
> pixdim4 0.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 0.0000
> funused1 1.0000
> funused2 0.0000
> funused3 0.0000
> cal_max 0.0000
> cal_min 0.0000
> compressed 0
> verified 0
> glmax 10505
> glmin 0
> descrip
> aux_file
> orient 0
> originator
> origin1 0
> origin2 0
> origin3 0
> generated
> scannum
> patient_id
> exp_date
> exp_time
> hist_un0
> views 0
> vols_added 0
> start_field 0
> field_skip 0
> omax 0
> omin 0
> smin 0
> smin 0
> file_type ANALYZE-7.5
> file_code 0
>
>
> On Mon, Jan 10, 2011 at 2:10 PM, Mark Jenkinson <[log in to unmask]> wrote:
> Hi,
>
> I don't have any problems doing the same thing at this end.
> I can't see anything obvious that you are doing wrong.
>
> Are you running the most recent version of FSL (4.1.6)?
>
> If so, do you get the usage message immediately, or
> after some computation?
>
> Also, can you send us the result of running fslerrorreport ?
> And let us know what platform/OS you are running this on.
>
> All the best,
> Mark
>
>
>
> On 10 Jan 2011, at 17:35, Graeme Schwindt wrote:
>
> > Hi Mark,
> >
> > Here is a copy-paste from the terminal below, as you can see it simply returns the usage of sienax, as if I had not correctly specified options. The odd thing is, running with -R in the quotes runs fine. Is it something about the spaces? Or am I missing something bone-headedly obvious
> >
> > prompt$ sienax test_sienax.img -B "-f 0.2"
> >
> > Usage: sienax <input> [options]
> >
> > -o <output-dir> : set output directory (default output is <input>_sienax)
> > -d : debug (don't delete intermediate files)
> > -B "betopts" : options to pass to BET brain extraction (inside double-quotes), e.g. -B "-f 0.3"
> > -2 : two-class segmentation (don't segment grey and white matter separately)
> > -t2 : T2-weighted input image (default T1-weighted)
> > -t <t> : ignore from t (mm) upwards in MNI152/Talairach space
> > -b <b> : ignore from b (mm) downwards in MNI152/Talairach space (b should probably be negative)
> > -r : regional - use standard-space masks to give peripheral cortex GM volume (3-class segmentation only) and ventricular CSF volume
> > -lm <mask> : use lesion (or lesion+CSF) mask to remove incorrectly labelled "grey matter" voxels
> > -S "segopts" : options to pass to FAST segmentation (inside double-quotes), e.g. -S "-i 20"
> >
> > On Mon, Jan 10, 2011 at 12:15 PM, Mark Jenkinson <[log in to unmask]> wrote:
> > Hi,
> >
> > OK, the bash script will be complicated.
> > However, calling it from the command line should work fine.
> > Can you give me the exact command you are running and the
> > exact error output?
> >
> > All the best,
> > Mark
> >
> >
> > On 10 Jan 2011, at 17:14, Graeme Schwindt wrote:
> >
> > > Hi Mark,
> > >
> > > Thanks for your reply. This is simply running from the command line, or calling it from within a bash script, so it seems there is something going on. We're running fsl 4.1
> > >
> > > On Mon, Jan 10, 2011 at 12:08 PM, Mark Jenkinson <[log in to unmask]> wrote:
> > > Hi,
> > >
> > > Are you doing this from within a script or trying to run it on a cluster?
> > > That can make it difficult with the quotes.
> > >
> > > If you are using fsl_sub to run it on a cluster then I recommend
> > > using the -t option and putting the command, with quotes as usual,
> > > into the file that is specified by -t. This will run it correctly on the
> > > cluster.
> > >
> > > If you are doing it within your own script then it is trickier, but
> > > running it with the fsl_sub and -t is still an option, although
> > > you will need to make any subsequent commands that depend
> > > on the output run with another fsl_sub job that has a hold on
> > > the first job number.
> > >
> > > If you are running this directly on the command line and still
> > > having trouble then please let us know, as that would indicate
> > > more fundamental problems.
> > >
> > > All the best,
> > > Mark
> > >
> > >
> > >
> > > On 10 Jan 2011, at 15:49, Graeme Schwindt wrote:
> > >
> > > > I'm having some odd trouble with getting sienax to run with -B options
> > > >
> > > > Command is: sienax patient_T1.img -B "-f 0.2"
> > > >
> > > > But simply returns the usage, indicating some kind of error in the command - anyone have any clue what's going on? It will run fine with "-R" in quotes, but trying to change f is not working....
> > > >
> > > > Thanks
> > > >
> > > > Graeme
> > >
> > >
> > >
> > > --
> > > Graeme C. Schwindt, HBSc
> > > MD/PhD Student
> > > University of Toronto
> > > [log in to unmask]
> > >
> >
> >
> >
> > --
> > Graeme C. Schwindt, HBSc
> > MD/PhD Student
> > University of Toronto
> > [log in to unmask]
> >
>
>
>
> --
> Graeme C. Schwindt, HBSc
> MD/PhD Student
> University of Toronto
> [log in to unmask]
>
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