[MINC-users] best_nonlin_reg.pl ?

Fri Apr 8 17:27:41 EDT 2011

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
>
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Checking a XFM file (init-0024-16647_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
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Checking a MINC file (init-0025-16702_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0025-16702_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0026-16706_001_MNI152maskedout_RAS_nu_mincnorm_bestlinreg_nihpd_new_grid_0.mnc)
0
Checking a XFM file (init-0026-16706_001_MNI152maskedout_RAS_nu_mincnorm_bestlinreg_nihpd_new.xfm)
0
Checking a MINC file (init-0027-16734_001_MNI152maskedout_RAS_nu_mincnorm_bestlinreg_nihpd_new_grid_0.mnc)
0
Checking a XFM file (init-0027-16734_001_MNI152maskedout_RAS_nu_mincnorm_bestlinreg_nihpd_new.xfm)
0
Checking a MINC file (init-0028-SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0028-SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0029-SEA0094_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0029-SEA0094_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0030-SEA0102_6mo_Sep2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0030-SEA0102_6mo_Sep2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0031-SEA0111_6mo_Dec2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0031-SEA0111_6mo_Dec2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0032-SEA0112_6mo_Dec2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0032-SEA0112_6mo_Dec2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0033-SEA0120_6mo_Mar2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0033-SEA0120_6mo_Mar2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0034-SEA0124_6mo_Mar2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0034-SEA0124_6mo_Mar2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0035-SEA0135_6mo_June2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0035-SEA0135_6mo_June2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0036-SEA0136_6mo_May2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0036-SEA0136_6mo_May2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0037-SEA0141_6mo_July2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0037-SEA0141_6mo_July2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0038-SEA0152_6mo_Dec2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0038-SEA0152_6mo_Dec2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0039-SEA0153_7mo_Dec2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0039-SEA0153_7mo_Dec2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0040-SEA0154_6mo_Dec2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0040-SEA0154_6mo_Dec2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0041-SEA0157_6mo_Jan2011_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0041-SEA0157_6mo_Jan2011_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0042-SEA0158_6mo_Jan2011_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0042-SEA0158_6mo_Jan2011_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0