Hi,
well, I suggested several options and I guess you will have to find out
which one works best in your setting, for your project, with your
computer. I am not sure which option would be best for you but using the
standard brainmask is probably the one I would have tried last (mostly
because I am usually performing my first level analyses in native space).
Cheers,
Marko
monika grewal wrote:
> Thank you Marko.
>
> I read something about using brainmask.nii as analysis mask(link given
> below). Although, there are other proposed methods also to generate
> whole brain mask but, i want to try this one first because it seems to
> be the easiest one.
> Please suggest if you know any other more effective method.
>
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;a3089d1f.1009
>
>
> On Tue, May 7, 2013 at 3:15 PM, Marko Wilke
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hello,
>
> glad one of my suggestions worked for you. However, I do not think
> you can easily dismiss those brain regions excluded by the higher
> threshold as "certainly not being activated". I would recommend you
> generate an appropriate mask including all your voxels and redo the
> analyses. The fact alone that the search volume is different may
> influence your pattern of activation (smoothness estimation, number
> of multiple comparisons to correct for etc.), I therefore don't
> think you should go ahead with what you have.
>
> Cheers,
> Marko
>
> monika grewal wrote:
>
> Thanks Marko.
>
> I had tried looking into my raw data and that seemed to be perfectly
> fine. Now, when i changed threshold masking value in
> spm_defaults.m from
> 80% to 70%, the new mask.img is decent enough.
> That means it was due to this threshold masking only. But, i
> still want
> to clear if i am right in saying that these missing voxels in
> mask.img
> actually had intensity values less than 80% of global signal. Hence,
> there's no chance of them being activated. Therefore, even if i
> change
> threshold masking default value, my results won't be affected much
> (considering that i'm not much interested in looking for
> deactivations).
> So, i can easily interpret my results based on present analysis
> threshold only.
>
> Or else, should i lower down my threshold masking value and look for
> deactivations in this right hemispheric region.
>
> Regards,
> M. Grewal
>
>
> On Tue, May 7, 2013 at 12:58 PM, Marko Wilke
> <[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>> wrote:
>
> Hello M.,
>
> as you discovered, the generation of the mask relies on all
> voxels
> being interpretable in all volumes. Hence, if your final
> mask is
> missing voxels, spm for some reasons thinks it should not
> use those
> voxels, either because they are missing or because they are not
> interpretable in at least one image. Therefore, the first
> thing to
> do (which you probably did) is to check the raw data very
> closely.
> If you cannot find the offending volume, you can play with the
> masking options on the second level by including an
> implicit mask,
> and/or by disabling threshold masking and implicit masking.
> Not sure
> that playing with defaults (mask thresh or so) will help,
> but maybe
> worth a try. After you find the reason, you will then have
> to think
> again how appropriate your approach was :)
>
> Cheers,
> Marko
>
>
>
>
> M. grewal wrote:
>
> Hello SPMers,
>
> In my block design task, i was getting clear left
> lateralization. While scrolling through individual
> subject data,
> i noticed that it is not actually so, but merely due to
> a major
> part of right hemisphere being chopped out in final
> spmT images.
> Also, i noticed that it is because beta images have NaN
> values
> at those voxels in right hemisphere (one jpeg image
> attached
> hereby).
>
> Well, i understand that it is because of implicit
> masking which
> makes a particular voxel in all volumes either 0 or NaN
> (based
> on data representation scheme) if its value can't be
> sampled in
> one volume. No issues if its just one or two voxels. My
> concern
> here is a big chunk of voxels specifically in right
> hemisphere.
> Also, this empty voxel effect is consistent over 12
> subjects.
> So i'm concerning if its some sort of acquisition issue or
> realignment algorithm issue (well, i'm following
> standard SPM8
> protocol with most of the defaults intact).
> Also, i have removed implicit masking at realignment and
> smoothing stage. But, i feel this is somehow introduced
> at model
> estimation level while generating mask.img always. I
> want to
> know if i could control how mask.img is being
> calculated and
> modify any thresholding value to include more voxels in
> analysis. Also, i'm not sure how much appropriate that
> procedure
> would be.
>
> Please help..
>
>
> --
> ________________________________________________________
>
> 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 <tel:%2B49%207071%2029-83416>
> <tel:%2B49%207071%2029-83416>
> Fax +49 7071 29-5473 <tel:%2B49%207071%2029-5473>
> <tel:%2B49%207071%2029-5473>
> [log in to unmask]
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
>
> http://www.medizin.uni-____tuebingen.de/kinder/epn/
> <http://www.medizin.uni-__tuebingen.de/kinder/epn/>
> <http://www.medizin.uni-__tuebingen.de/kinder/epn/
> <http://www.medizin.uni-tuebingen.de/kinder/epn/>>
> ________________________________________________________
>
>
>
>
>
> --
>
> Monika Grewal
>
> R&D Engineer,
> National Brain Research Center,
> Gurgaon.
>
>
> --
> ______________________________________________________
> 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 <tel:%2B49%207071%2029-83416>
> Fax +49 7071 29-5473 <tel:%2B49%207071%2029-5473>
> [log in to unmask]
> <mailto:[log in to unmask]>
>
> http://www.medizin.uni-__tuebingen.de/kinder/epn/
> <http://www.medizin.uni-tuebingen.de/kinder/epn/>
> ______________________________________________________
>
>
>
>
> --
>
> Monika Grewal
>
> R&D Engineer,
> National Brain Research Center,
> Gurgaon.
--
____________________________________________________
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/
____________________________________________________
|
