Dear Adil,
The key lines are in the report.sienax file. They are:
Initial K-means segmentation...
8 main iterations ...
Estimating PVE...
new: Out of Memory!
So it looks like your machine is running out of memory.
As your images are 512x512x190 then they will take
190MB in memory each, which is not very much.
Do you have much memory on your machine?
And you say that FAST works on a GE image - is it
the same size? Does FAST work on your image
from the Philips scanner?
All the best,
Mark
On 16 Dec 2009, at 02:40, Adil Javed wrote:
> 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
>> or entity to which it is addressed and may contain
>> information that is privileged and confidential. If the
>> reader of this email message is not the intended recipient,
>> you are hereby notified that any dissemination,
>> distribution, or copying of this communication is
>> prohibited. If you have received this email in error, please
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>>
> <report.sienax>
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