On Fri, Nov 2, 2012 at 12:41 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

If this is a surface based analysis, then you'll need to add --surface fsaverage rh
doug

On 11/02/2012 11:34 AM, Ryan wrote:

Doug,
I ran: mri-glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh --fsgd fsgd doss --C training-effect.mtx

On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

On 11/01/2012 06:35 PM, Ryan wrote:

Doug,
Picture 4 shows the difference between the medial surface
for this analysis and for another type of analysis (where I
created my own matrix file) that completed normally. Is this
normal? I have never looked at this surface for errors before,
which is why I ask.

That is normal. Usually, the medial wall is masked out.

Picture 5 shows the command you just requested I run, and
all points across the cortical mantle look like this image -
nothing seems to be at exactly the same level.

That looks normal. What is your mri_glmfit command-line? Not the
mri_glmfit-sim cmd line.

On Thu, Nov 1, 2012 at 5:55 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

The mask looks ok to me (I did not notice anything strange
around
the CC). How do the sig maps look? Is there any data set
in there
that is odd? you can evaluate this with

tksurfer fsaverage lh inflated -ov glmdir/mask.mgh
-fminmax .5 1-t
y.mgh

this will bring up a "time" course where each point is an
input.
See if there are any inputs that are always 0 or some
other outlier.

doug

On 11/01/2012 04:50 PM, Ryan wrote:

Doug,

I attached the tksurfer images that I get with your
command, the area around the corpus callosum is oddly
yellow.
What caused this mask problem, and how can I fix it?
Thanks.

On Thu, Nov 1, 2012 at 2:55 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

The problem is that the fwhm is not-a-number
(glmdir/fwhm.dat).
Usually this means that there is something messed
up with
the mask
(glmdir/mask.mgh). View the mask to see what is up
tksurfer fsaverage lh inflated -ov glmdir/mask.mgh
-fminmax .5 1
doug

On 11/01/2012 02:39 PM, Ryan wrote:

Doug,
Here are the files.

On Thu, Nov 1, 2012 at 2:00 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:

Can you send the command line and attach
the files?
thanks
doug

On 11/01/2012 01:11 PM, Ryan wrote:

Doug,
I tried running mri_glmfit-sim
without the --bg
flag and it
finished in 10 minutes without any errors.
This has never
happened before, so I highly suspect these
results. Do you
know what could be wrong? In case you
need it,
the summary
file output and terminal output are
attached.

-Ryan

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
Phone Number: 617-724-2358
<tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>>
<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358>

<tel:617-724-2358 <tel:617-724-2358>>>>

Fax: 617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422

<tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422>

<tel:617-726-7422 <tel:617-726-7422>>

<tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>>>

Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

The information in this e-mail is intended
only
for the
person to
whom it is
addressed. If you believe this e-mail was
sent to
you in
error and
the e-mail
contains patient information, please
contact the
Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information,
please
contact the
sender and properly
dispose of the e-mail.

-- -Ryan

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>>
Fax: 617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
<tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>

Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

-- -Ryan

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

-- -Ryan

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

--
-Ryan

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

--
-Ryan