What were your scan parameters? Maybe the resolution is poor in all but one orientation, and that's why it looks bad in the other orientations.
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From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Marko Wilke [[log in to unmask]]
Sent: Thursday, January 26, 2012 7:36 AM
To: [log in to unmask]
Subject: Re: [SPM] WG: [SPM] T1 data suitability for VBM
Hi Couto,
for starters, I would suggest you try another DICOM converter (maybe the
one coming with spm...) to see if you still have these issues. Also, one
of the reasons you only have "nice" data in one dimension may be that
you do not have a 3D acquisition and that the other images represent
reformatted versions of that, but I can't tell from a distance. In any
case, as a rule of thumb I would say that, if the data does not look
good to the naked eye, it is not likely to be suitable for a VBM analysis :)
Cheers,
Marko
Couto, Blas wrote:
> -----Ursprüngliche Nachricht-----
> Von: Couto, Blas
> Gesendet: Donnerstag, 26. Januar 2012 12:17
> An: [log in to unmask]
> Betreff: WG: [SPM] T1 data suitability for VBM
>
> Dear Christopher,
>
> thanks for your response. I do want the not- o* and not- co* images, though while doing the conversion, besides this two types of files, I have as output 3 other .nii which contains slices. However, this slices happens to be of good quality in just one of the orientations (e.g sagittal) but not in the other 2, and so on with the three files.nii. Would you have any idea why this is working so? And why I do not have a single 3D volume with the 3 orientations of suitable (or at least similar) quality of voxel?
>
> Thankyou in advance, again.
> Kind regards,
> Blas Couto
>
> -----Ursprüngliche Nachricht-----
> Von: Chris Watson [mailto:[log in to unmask]]
> Gesendet: Mittwoch, 25. Januar 2012 20:05
> An: Couto, Blas
> Cc: [log in to unmask]
> Betreff: Re: [SPM] T1 data suitability for VBM
>
> I believe you want the image that is not the o* or co* image. On my system, the output filename is the study protocol that is entered on the scanner, so it would output e.g.
> STUDY.nii
> oSTUDY.nii
> coSTUDY.nii
>
> Couto, Blas wrote:
>>
>> Dear collegues,
>>
>>
>>
>> I have a sample data of structural MRIs, and I would like to try a VBM
>> analysis. However, while converting DICOM files to nifti (using Chris
>> Rorden´s software dcm2nii ), my output files are 2 or more .nii
>> containing either sagital, coronal or axial T1 oriented slices. I
>> would like to know if they are all/either suitable for SPM VBM analysis?
>>
>>
>>
>> Thank you all in advance.
>>
>> Best regards,
>>
>>
>>
>> Blas Couto
>>
>>
>>
>>
>>
>> _________________________________________________________
>>
>> *Juan Blas Marcos Couto, M.D.*
>>
>> *Researcher*
>>
>> *Laboratory of Experimental Psychology& Neuroscience*
>>
>> *Institute of Cognitive Neurology (INECO)& CONICET*
>>
>> *Pacheco de Melo 1854/60 (C1126AAB)
>> Buenos Aires, Argentina
>> Phone/Fax: +54 (11) 4812-0010*
>>
>>
>>
>
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn
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