On Tue, May 6, 2014 at 2:41 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Is the cortex label 0 in the same locations where you have 0s in the surface mask?

On 05/06/2014 12:07 PM, Cesar Echavarria wrote:

Hi Doug,

Me and Shahin have looked at the registration and it looks fine. I know the activation is 0 because when I click on those vertices it tells me the tksconcat.nii value is "**0.000000**". I looked at the cortex.label file and found the 0-valued vertices within the file. We have scanned the same subject for different experiments but it is only for this session that we find the problem. Let me know if there's anything else we can check.

Thanks!
Cesar

On Mon, May 5, 2014 at 6:04 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Have you checked the registration? If so, are you sure that the
activation is exactly 0? Also, look at cortex.label to check
whether somehow those vertices were not labeled.

On 05/05/2014 04:08 PM, Cesar Echavarria wrote:

I used the command below to check the brain mask relative to
the subject's anatomy:

tkmedit myla_anat orig.mgz -over
Subjects/myla/bold/masks/brain.nii.gz

The mask looked fine in that no portion of the brain appeared
to lie outside the mask.

Cesar

On Mon, May 5, 2014 at 3:43 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:

It could be that the brain mask is too aggressive. Try
looking at
Subjects/myla/bold/RRR/masks/brain.nii.gz

doug

On 05/05/2014 03:17 PM, Cesar Echavarria wrote:

Hi Bruce,

After unpacking the data, I simply run the selxavg command
below and allow it to do the automatic pre-processing.

selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh

The analysis was generated with the following command:

mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface
fsaverage rh -fwhm 5 -paradigm LOC.par -event-related
-polyfit
1 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 2
-refeventdur 16 -per-run -force -fsd bold

After fixing up the registration I saved the
registration file
under :Subjects/myla/bold/014/register.dof6.dat" and ran
bbregister for all the runs within the subject folder
as below.

bbregister --mov Subjects/myla/bold/015/f.nii --reg
Subjects/myla/bold/015/register.dof6.dat --init-reg
Subjects/myla/bold/014/register.dof6.dat --bold

I then ran the selxavg3-sess again.

Let me know if you need any more information to help.

Thanks!
Cesar

On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>
<mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>

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

Hi Cesar

what command lines did you run to register and sample?

Bruce

On Mon, 5 May 2014, Cesar Echavarria wrote:

Hello freesurfer experts,
The functional overlay for one of our subjects
looks
like the
image attached. You'll notice
the "holes" on the overlay that have a value
of 0. I'm
trying
to get ride of these as I
expect (as with other subjects) to have values
for these
vertices that are not 0. Myself and
a colleague have tried improving the
registration as
much as
we see possible, but the problem
remains. Any tips on how to correct this issue
would be
greatly appreciated.

Thanks in advance for your help!
[cleardot.gif]
Cesar Echavarria
Research AssistantMartinos Center for
Biomedical Imaging,
Harvard-MGH

Brain & Cognitive Sciences | MIT 2012

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>

<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.

-- Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012

-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2
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>

Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012

-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

--
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012

--
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Cesar Echavarria
Research Assistant

Martinos Center for Biomedical Imaging, Harvard-MGH

Brain & Cognitive Sciences | MIT 2012