Hi Suzanne, there is probably an easier way to do this. If you create contrasts of each condition vs baseline then run isxconcat-sess on each, you can then run something like

mri_segstats --seg mc-z.pos.23.lh.sig.ocn.mgh --i condition1.nii.gz --avgwf condition1.table.dat --excludeid 0

where condition1.nii.gz is the output of isxconcat-sess for condition 1. The output fo mri_segstats will be condition1.table.dat which will have a row for each subject and a column for each of the clusters

doug

On 11/01/2013 09:51 AM, Suzanne Oosterwijk wrote:

Hello again,

I am stuck again in my analysis and I am not sure that my code is right. I want to do the following. With a Monte Carlo simulation I search for significant clusters within a particular ROI in my all conditions vs baseline contrast. Then I want to translate this functional cluster to each individuals native space (as a label) and extract percent signal change for each condition separately from that label. This is no problem in my surface analysis, but I am not sure how to do this in the volume. I ran the Monte Carlo simulation within the mask, which provides a segmentation called mc-z.pos.23.lh.sig.ocn.mgh. I assume that this would be the label that would go into mri_vol2vol to translate the cluster to native space. I found on the website, however, that you need to use tkregister first. So I used the following code, but I am doubtful about whether I am doing this right.

tkregister2 --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --s ff_01_030512 --regheader --reg ff_01_030512/register.dat --surf

The results of this command do not look good at all....(see attached image). The cluster in the -mov file does not overlap with the amygdala. For the next step, I assumed to use mri_vol2vol to save the cluster as a native space label, although I'd like to make sure the first step is correct before continuing with this step.

mri_vol2vol --mov /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol

/omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --reg ff_01_030512/register.dat --fstarg --interp nearest --o ff_01_030512/label/lh.amygdala.imact.mgz --s ff_01_030512


What am I missing? Is the translation off because I did something wrong, or does that point to a deeper issue?


Any help is much appreciated!


Suzanne

On Tue, Oct 29, 2013 at 6:04 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Hi suzanne, you'll need to use the 2mm version
    fsaverage/mri.2mm/aseg.mgz
    doug

    On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote:
    > Hello all,
    >
    > I want to run a Monte Carlo simulation within a volume ROI and I am
    > running into a problem when I use the --mask flag while running
    > glmfit. My question is very similar to the question asked in
    > "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask
    > area" but I could not find the response to this question.
    >
    > Here is my code.
    >
    > First, I created a volume mask with mri_binarize:
    >
    > mri_binarize --match 18 --i
    >
    home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz
    > --o
    >
    /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
    >
    > I checked the mask and it looked good. Then I use the mask in
    glmfit.
    >
    > mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask
    >
    /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
    >
    > When I do this, I get the following error:
    >
    > ERROR: dimension mismatch 1 between y and mask
    >
    > I guess this means that the ces.nii.gz file and mask file don't
    match,
    > but I have no idea how to solve this. Any thoughts?
    >
    > Thanks!
    > Suzanne
    >
    >
    > --
    >
    > Suzanne Oosterwijk, Ph.D.
    >
    > Postdoctoral Researcher
    >
    > Department of Social Psychology
    >
    > University of Amsterdam
    >
    > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu

    <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> <http://va.nl>

    >
    > https://sites.google.com/site/suzanneoosterwijk/
    >
    >
    >
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu

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

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

    --
    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/

    _______________________________________________
    Freesurfer mailing list

    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.




--

Suzanne Oosterwijk, Ph.D.

Postdoctoral Researcher

Department of Social Psychology

University of Amsterdam

s.oosterwijk@u <mailto:s.oosterwijk@neu.edu>va.nl <http://va.nl>

https://sites.google.com/site/suzanneoosterwijk/

--
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/