trying to import dicom files

[labolisa]

hello !

I have tried to import an mri T1 image and succeeded with Import irm T1 and Aims Converter

Next, I've try to import PET (tep) images with the two previous methods and it fails.

I've also try with AimsFileConvert directly :

/usr/local/etc/SHFJ_pack-stable-linux-2.3.5/bin/AimsFileConvert -i ../../../p3_se7/im1 -o img_irm.ima
filein : ../../../p3_se7/im1
fileout : img_irm.ima
ascii : 0
rescale : 0
format :
type :
objtype :
xdim : 0
ydim : 0
zdim : 0 %%%% it stopped here for pet images
reading ../../../p3_se7/im1 as Volume / S16...
reading done
converting data...
convert done
writing img_irm.ima...
done

One of my test has running on during 18 hours and wasn't finished.

What can I do ?

[Manik]

Hello,

is this a DICOM image ?
If so, I had problems with some dicom images. You should try to convert it to GIS format or another format known to BrainVisa (SPM, for example) using another tool.

[Guidon]

Importing data should take a minute or so. Having a process hanging for 18 hours is synonym of a crash. There are some explanations on the forum about setting the proper environment on Linux to prevent the processes from hanging. Since I run a mac, I just keep a task manager open in order to keep an eye on the processor activity and I force quit the application when the Aims* process is lazy.

Apart from that, I have never tried to import PET dicom.

[labolisa]

thanks, but the only reason that push me to use this command is to convert my dicom in GIS format. I'll find a soft for convert it. Do you know one?
(I think I've a problem with my dicom header too)

[riviere]

thanks, but the only reason that push me to use this command is to convert my dicom in GIS format. I'll find a soft for convert it. Do you know one?
(I think I've a problem with my dicom header too)

Yes, there are several: XMedCon or MRIcro could do it I guess.

I force quit the application when the Aims* process is lazy

Oooh, does it happen often ? You're frightening me... I experienced (and documented) such hangs when Brainvisa is run from the Mac Finder (icon double-click) but seemed to run well when launched from a terminal. I have never found any explanation for this curious phenomenon but we don't have any Mac experts in the lab...

Denis

[Yann Cointepas]

I already encountered problems with DICOM PET images encoded in only one file. Our implementation of DICOM reader is not complete and can only work with one file per slice. If a whole 3D or 4D volume is stored in only one file, Aims (and therefore Anatomist) are not able to read it.

Unfortunately, we do not have enough time to fix this for the next release (developpement is stopped on monday).

[labolisa]

ok thank you I will use mricro

I know PET format isn't so current, so don't be sorry

good luck for your following releases

[Guidon]

Oooh, does it happen often ? You're frightening me... I experienced (and documented) such hangs when Brainvisa is run from the Mac Finder (icon double-click) but seemed to run well when launched from a terminal. I have never found any explanation for this curious phenomenon but we don't have any Mac experts in the lab...
Denis

Hi Denis,

I usually run brainvisa from the dock, which might just be considered as a finder shortcut. I didn't know that it was safer to run brainvisa from a Terminal but from now on I will do so and I will let ou know in case it hangs again.
Previously, when I launched brainvisa from the dock icon, the application would systematically hang after I ran one or two processes.

[riviere]

Hangs from the dock or the finder is also what we get. But so far I haven't seen it hang when run from a term. I don't have the slightest idea of what could explain it. If anybody has a clue, just tell me...
Or if you also experience hangs from a term, tell me too, so that I can at least list it in the known problems list...
Denis