Hi Donna,
Thanks for testing this, and for your fast response. Yes we're not
getting a core dump and it does finish, although with 144 cycles. Are
you saying we should switch back to the old caret for the time being? I
mean, the check_reg result seems fine, but maybe there's still something
wrong with it?
Thank you!
--ts
On 11/27/2013 11:27 AM, Donna Dierker wrote:
Hi Taosheng,
I tried running postborder.sh on a dataset I have here, and I got a core dump
on the offending line:
+ caret_command -surface-sphere-multi-morph Human.SAIS_018.L.73730.spec
deformed_Human.SAIS_018.L.Midthickness_711-2B.mws.coord
Human.SAIS_018.L.SPHERICAL.73730.MWS.coord Human.SAIS_018.L.CLOSED.73730.topo
./PALS_B12.LR/postborder.sh: line 50: 27257 Segmentation fault (core
dumped) caret_command -surface-sphere-multi-morph $SPEC $FIDUCIAL_MWS
$SPHERE_MWS $TOPO
You're not getting a core dump, but something else is clearly going awry with
that line.
I tried backtracking to a June 2011 vintage caret, and it completed with no
problems. Here is the version I used:
http://brainvis.wustl.edu/pub/caret/caret_distribution_Linux64.v5.64.zip
login pub
password download
Here are the logs for the for the two versions of caret (bad and good):
Problem log:
http://brainmap.wustl.edu/pub/donna/US/MI/postborder.log
Good log:
http://brainvis.wustl.edu/pub/donna/US/MI/postborder.201106.log
I'm not sure when caret_command will be fixed, but I will pass the dataset and
details on to the developers.
Donna
On Nov 26, 2013, at 11:58 AM, Donna Dierker <[email protected]> wrote:
Hi Taosheng,
I am going to try postborder.sh on my new Linux box and see if it does the same
thing.
I don't see any candidate culprits in my ~/.caret5_preferences file.
No one else has reported this issue. More users are moving to the fs_LR
pipeline:
http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs_LR
There are trade-offs which are discussed here:
http://cercor.oxfordjournals.org/content/early/2011/11/02/cercor.bhr291.full.pdf+html
One big plus is that there is no border tweaking.
I'll let you know how my post border.sh trial comes out, or if I need sample
data. But I think I have plenty of sample data right here. I can't imagine
what might be unique about our data that would cause this.
Donna
On Nov 26, 2013, at 8:22 AM, Taosheng Liu <[email protected]> wrote:
Hi Donna,
Yes I can see that line of code in the script. Have you other others on this
list run this command lately? I wonder if you also see this many cycles. If
not, I wonder if there is some global setting I should set, or something is off
with my data. I can certainly supply the data if needed.
Thank you,
--Taosheng
On 11/25/2013 06:50 PM, Donna Dierker wrote:
Hmmm. Your results look great, but 144 cycles of spherical morphing is
certainly not normal. I think the line in the script that does this is this
one:
#MULTIRESOLUTION MORPHING
caret_command -surface-sphere-multi-morph $SPEC $FIDUCIAL_MWS $SPHERE_MWS
$TOPO
There are no parameters for this one; they are built in, apparently, so I'm not
sure what could be going on.
I'm stumped.
On Nov 25, 2013, at 4:27 PM, Taosheng Liu <[email protected]> wrote:
Hi Donna,
I've been using the preborder and postborder scripts to convert files from
FreeSurfer to Caret (hope you still remember I was involved in early testing of
these scripts). Things have been working great. I haven't done this for a
while, but recently I changed computer and installed the current version of
Caret and these scripts, and there seems to be some difference in how the code
works. I just want to make sure this is expected behavior.
Specifically, when we run postborder script, it takes much longer. It seems
either the script or caret_command is doing more iterations, because we now see
files like this after the script finishes:
Human.FS040.L.SPHERICAL.73730.MWS.SPHERE_CYCLE144.coord
There're a lot of files like this, with consecutive names from CYCLE1 to CYCLE
144, whereas previously it only goes from CYCLE1 to CYCLE4. My question is: is
this expected behavior, or is there something wrong in how we ran the scripts?
I've posted the result from the check_reg here
http://psychology.msu.edu/liulab/files/html_out/views.html
They look just like before, but I'd like to confirm whether this is normal.
Thank you very much,
--Taosheng
--
Taosheng Liu
Assistant Professor
Department of Psychology
Michigan State University
316 Physics Road
East Lansing, MI 48824
PH: 517.432.6694
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
--
Taosheng Liu
Assistant Professor
Department of Psychology
Michigan State University
316 Physics Road
East Lansing, MI 48824
PH: 517.432.6694
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
--
Taosheng Liu
Assistant Professor
Department of Psychology
Michigan State University
316 Physics Road
East Lansing, MI 48824
PH: 517.432.6694
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
