Hi,
when I run sienax on a GE obtained T1 3D FSPGR image, it runs fine. But when I run sienax on a philips scanner obtained T1 3D SPGR image, it gives me error listed below. The sienax.report is also attached. Not sure what's going on. Thanks for your help.
aj
error shown in terminal:
[AJ@localhost Desktop]$ sienax '/home/AJ/Desktop/ZS__9608079_801_3D_SENSE_SPGR_20090317.nii'
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1): bad header info
Error: failed to open file I_stdmaskbrain_pve_1
ERROR: Could not open image I_stdmaskbrain_pve_1
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_1
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_2'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_2): bad header info
Error: failed to open file I_stdmaskbrain_pve_2
ERROR: Could not open image I_stdmaskbrain_pve_2
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_2
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_seg'
** ERROR: nifti_image_open(I_stdmaskbrain_seg): bad header info
Error: failed to open file I_stdmaskbrain_seg
ERROR: Could not open image I_stdmaskbrain_seg
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/sienax: line 283: 7599 Aborted ${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_stdmaskbrain_seg 1.9 5 ${I}_render
** ERROR (nifti_image_read): failed to find header file for 'I_render'
** ERROR: nifti_image_open(I_render): bad header info
Error: failed to open file I_render
ERROR: Could not open image I_render
Image Exception : #22 :: Failed to read volume I_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/sienax: line 284: 7600 Aborted ${FSLDIR}/bin/slicer ${I}_render -s 1 -x 0.4 gr${I}a.png -x 0.5 gr${I}b.png -x 0.6 gr${I}c.png -y 0.4 gr${I}d.png -y 0.5 gr${I}e.png -y 0.6 gr${I}f.png -z 0.4 gr${I}g.png -z 0.5 gr${I}h.png -z 0.6 gr${I}i.png
Cannot open grIa.png for reading
/usr/local/fsl/bin/sienax: line 285: 7601 Segmentation fault ${FSLDIR}/bin/pngappend gr${I}a.png + gr${I}b.png + gr${I}c.png + gr${I}d.png + gr${I}e.png + gr${I}f.png + gr${I}g.png + gr${I}h.png + gr${I}i.png ${I}_render.png
/bin/rm: cannot remove `grI?.???': No such file or directory
Finished. The SIENAX report can be viewed by pointing your web browser at:
file:/home/AJ/Desktop/ZS__9608079_801_3D_SENSE_SPGR_20090317_sienax/report.html
Estimated normalised brain volume (NBV) =
3.02
--- On Tue, 12/15/09, Javed, Adil [BSD] - NEU <[log in to unmask]> wrote:
> From: Javed, Adil [BSD] - NEU <[log in to unmask]>
> Subject: FW: [FSL] sienax issue
> To: [log in to unmask]
> Date: Tuesday, December 15, 2009, 8:30 PM
>
>
>
>
>
> FW: [FSL] sienax issue
>
> -----Original Message-----
>
> From: FSL - FMRIB's Software Library on behalf of Mark
> Jenkinson
>
> Sent: Tue 12/15/2009 4:27 AM
>
> To: [log in to unmask]
>
> Subject: Re: [FSL] sienax issue
>
>
>
> Hi,
>
>
>
> Can you send us the contents of the report.sienax file?
>
> It is possible that something went wrong before FAST was
> run.
>
>
>
> Also, send us the output of "ls -l" on the
> directory where
>
> this was run.
>
>
>
> All the best,
>
> Mark
>
>
>
>
>
>
>
> On 14 Dec 2009, at 04:06, Adil Javed wrote:
>
>
>
> > Hi,
>
> > I am trying to run sienax on a T1 3D SPGR image, but
> it gives me an
>
> > error. I am able to run FAST on the same file. If
> someone could
>
> > please read the attached error file and see if you can
> figure this
>
> > out I would greatly appreciate it.
>
> > tx,
>
> > aj<sienax ouput.odt>
>
>
>
>
>
>
>
>
> This email is intended only for the use of the individual
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