Hi Yaroslav,<br><br>I'm a novice of fMRI and MVPA Analysis, I think you
want to know if those fields are congruent with Analyze format specially
if they are from SPM.<br>Well, the files I have are converted using Brain Voyager, so viewing the file you link it shouldn't have that problem. <br>
Checking my images with MRIcro and viewing fields on PyMVPA with command
mydataset.niftiheader.get() (Images loaded by list of NiftiImages!) I
found the same values:<br>scl_interp = 19 e scl_slope = 17; now my question is: Could I proceed with the analysis or I have to do other further steps?<br>
<br>Thank you<br>Roberto<br><div class="gmail_quote"><br><br><div class="gmail_quote">2011/3/3 Yaroslav Halchenko <span dir="ltr"><<a href="mailto:debian@onerussian.com" target="_blank">debian@onerussian.com</a>></span><div>
<div></div><div class="h5"><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Roberto,<br>
<br>
as we have discovered in our troubleshooting thread with Nynke van der<br>
Laan, in PyMVPA 0.4.x and 0.5.x series, while relying on pynifti<br>
interface to load data, we did not account for scaling/offset parameters<br>
encoded in Nifti headers. So, if those .hdr/.img correspond to Nifti<br>
files, you should better check if they have the same scl_inter/scl_slope<br>
values... if those correspond to Analyze files... it is even more<br>
interesting since then if it comes from SPM, according to<br>
<br>
<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/Analyze_usage.pdf" target="_blank">http://nifti.nimh.nih.gov/nifti-1/documentation/Analyze_usage.pdf</a><br>
<br>
those inter/slope could still have been encoded in some fields, and thus<br>
loaded data might not be appropriate for the analysis in PyMVPA. The<br>
best resolution would be to join them into a single 4D Nifti<br>
volume file (and double check if scaling/offsetting is done correctly by<br>
the software you would use for that)<br>
<br>
Tomorrow or on weekend we will make full announcement and fresh<br>
bugfix release of 0.4.x series which should take care about scaling<br>
issue.<br>
<br>
Meanwhile -- if you have 'Analyze' files -- would you mind forwarding me<br>
few samples to check on the status of their fields.<br>
<br>
With best regards,<br>
Yarik<br>
<div><br>
On Thu, 03 Mar 2011, Roberto Guidotti wrote:<br>
<br>
> Thank you Michael it works perfectly....<br>
> Sorry but I'm a novice with Python and this technique, I'm glad to have<br>
> the support of you and the other authorities of MVPA techniques!!<br>
> Thank you<br>
> Roberto<br>
<br>
</div>> 2011/3/1 Michael Hanke <[1]<a href="mailto:michael.hanke@gmail.com" target="_blank">michael.hanke@gmail.com</a>><br>
<div><br>
> On Mon, Feb 28, 2011 at 04:38:58PM +0100, Roberto Guidotti wrote:<br>
> > Dear all,<br>
<br>
> > I have to analyze some fmri data with pymvpa: my images are in<br>
> Analyze<br>
> > format: every volume is a .hdr .img pair and I have to load as a time<br>
> > series. How can I do?<br>
> > The solution is to convert my datasets with some software as MRIcro<br>
> or<br>
> > similar, but I want to know if there is a "library" solution to solve<br>
> that<br>
> > issue or if I could do this by building a script managing and merging<br>
> > several arrays.<br>
<br>
> You should be able to load them all one by one into a list of images<br>
> and<br>
> supply that list as an argument to the Dataset constructor. It<br>
> should<br>
> just work.<br>
> Michael<br>
> PS: Sorry for the delay<br>
--<br>
</div>=------------------------------------------------------------------=<br>
Keep in touch <a href="http://www.onerussian.com" target="_blank">www.onerussian.com</a><br>
<font color="#888888">Yaroslav Halchenko <a href="http://www.ohloh.net/accounts/yarikoptic" target="_blank">www.ohloh.net/accounts/yarikoptic</a><br>
</font><div><div></div><div><br>
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