[MINC-users] Concerns Re. Strange-looking MNC Output Files

[Sylvain MILOT]

Hello Shahin,

a few things ...

If you look at mripet_rsl/guizard_nicolas_200602161008_* with register,
you'll notice it is way off. I havent seen many of these over the years
since this process is very robust ... but it happens.

I would redo this one with 'do_mritopet -mritopet -tracc ...' see mritopet
-help for more info. First you should isolate this subject into a separate
directory to ease things with do_mritopet and do_pettopet and you can
easily do this with symlinks (ln -s). Verify the new results and then redo
the do_pettopet part for that subject only.

the recipe is:

cd /data/zlab/shahin/space-time2/analysis
mkdir new
cd new
mkdir mri pet mrital_xfm
(cd mri; ln -s ../../mri/guizard_nicolas_20060127_140219_2_mri.mnc .)
(cd pet; ln -s ../../pet/guizard_nicolas* .)
(cd mrital_xfm; ln -s ../../mrital_xfm/guizard_nicolas_mrital.xfm .)
do_mritopet -mritopet -tracc -batch
register mripet_rsl/*
# if good
batch do_pettopet
# if not good call me


Also in dot' s setup for this study, the mripet transformation file
is wrong for Lauren Klimoff - it should be
klimoff_lauren_200601050920_mripet.xfm. The one specified is based on the
transmission image.

Aside from that, your data is pretty noisy, ie lots of residual
uncorrected patient movement ... add to that the fact that your t-tests
are not very strong (ie testing normalized CBF with no possibility of
accounting for fixed subject effect) and that you probably shouldn't be
using a pooled sd measure ...

Sylvain

On Mon, 8 May 2006, Shahin Zangenehpour wrote:

> Dear All,
>
> I hope someone can help me with the following problem.
>
> I ran co-variation analyses using DOT on a number of experimental
> conditions (found in study "SpaceTime2" in /home/bic/shahin/dot/Dbase/
> Tables).
>
> The operations are labelled as "FCA2", "FCV21" and "FCV214", with
> their respective voi regressors labelled exactly the same way.
>
> The output files are stored in "/data/zlab/shahin/space-time2/
> analysis/output/stat/" and they all start with "SpaceTime2_stat_FC"
> followed by the appropriate strings for each condition (e.g., /data/
> zlab/shahin/space-time2/analysis/output/stat/
> SpaceTime2_stat_FCA2_FCA2.mnc).
>
> As you will note, the outcome of these operations have truncated
> volumes as opposed to other _stat_ files in the same folder. Sylvain
> has suggested in passing that there may be problems with the
> registration process or the transformation files. However, I don't
> have the slightest clue in how to go about identifying and
> subsequently solving such problems. Can anyone help directing me to
> the source? I hope I have provided all the essential information to
> track this down.
>
> Many thanks in advance,
> SZ
>
> ________________________________________________________________________
> _______________________________
> Shahin Zangenehpour, PhD    Postdoctoral Fellow   |   Montreal
> Neurological Institute   |   Cognitive Neuroscience Unit
> 3801 University Street   |   Room 276  |  Montréal   QC   Canada
> H3A 2B4  |   P.  514  398  1717  |  F.  514  398  1338
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (trinity at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4