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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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.oosterw...@neu.edu > <mailto:s.oosterw...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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.oosterw...@neu.edu>va.nl <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
