On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Greve <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>> 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>>> 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>>>> 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>>>
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>

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-- -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