[MINC-users] best_nonlin_reg.pl ?

[Lisa F. Akiyama]

Another question on making average models....

I've been creating several preliminary models using different configurations
and methods.
The MNI average brain models for both adults and pediatrics are all straight
in every direction.
However, I look at my resulting models, some of them are a tad tilted in one
or more directions. Going back and checking closely the individuals' scans
that were coregistered (linear 9 parameter registration) to a standard
template,
I find that a few of the coregistered images are slightly tilted. I suspect
that this is why the resulting average model is slightly tilted as well.
Is this a common issue faced when coregistering each individual to a
standard template and creating a model? If so, what are some of the common
ways of fixing them so that the resulting average model will be straight in
every direction and still keeping
the proper MNI space?

Thank you.


Best,
Lisa

On Fri, Apr 8, 2011 at 2:27 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> Hi Andrew,
>
> Thanks for your reply.
>
> I checked both runs of volgenmodel I was performing on the same set of data
> but with different configurations - one stopped at creation of working
> directory folder 03, the other stopping at folder 07.
> In both cases, I also checked the contents of all the folders that were
> created prior to 03 and 07, respectively, too, using the minccomplete
> command.
> However, in all cases, I got only got "0"'s, no "-1"'s. (Please see the
> attached text file for a copy of the results I got when running minccomplete
> in the 03 folder)
> I've removed the 03/07 folder and re-ran volgenmodel, but I still get the
> same error...
> When I run volgenmodel with the same configurations but with a different
> set of subjects, it runs fine...It is puzzling...
>
>
> Best,
> Lisa
>  ______________________________
> Lisa F. Akiyama
> Research Study Assistant
> Institute for Learning & Brain Sciences (I-LABS)
> University of Washington
> Portage Bay Building, BOX 357988
> Seattle, WA 98195-7988  U.S.A.
> E-mail: lrisa87 at uw.edu
>
> P Please consider the environment before printing this e-mail.
>
>
>
> On Thu, Apr 7, 2011 at 5:09 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Hi Lisa,
>>
>> > ...bestlinreg.xfm genmodel-work/07/avgxfm.xfm
>> >> Processing:........................miicv_attach: MINC package entry
>> point
>> >> ncvarid: ncid -1: NetCDF: Not a valid ID
>>
>> > I've tried using volgenmodel for two different fit.conf settings and get
>> the
>> > same error at
>> > about the same time point in the course of running this script.
>> > This error appears some point after the "07" folder and some, if not
>> all, of
>> > their contents are created in the working directory.
>> >
>> >  What could be some possible causes? Am I missing some other required
>> > script?
>>
>> I have tried to make volgenmodel as resistant to steps failing as I
>> can but it would seem that there is always one more thing that can go
>> wrong....  My guess is that you have an incomplete xfm file in the 07
>> step folder and this is causing xfmavg to fail.
>>
>> You can usually hunt down the culprit by going into this folder and
>> running minccomplete on all of the .mnc and .xfm files in there.
>>
>> ie:
>>
>>   $ ls *.mnc *.xfm | xargs -I {} minccomplete -verbose {}
>>
>> If any of the files return a -1 instead of 0 something went amiss. The
>> best approach at this stage is to just remove this file and re-run
>> volgenmodel at which point it should pick up where it left off.
>>
>>
>> a
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>