You can try it with tkmedit tkmedit fsaverage orig.mgz -overlay /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh
Also, in freeview try reducing the threshold to see if something pops up.
doug
Antonella Kis wrote:
Hi Doug,
Many thanks for your answer. Yes, there are four clusters as you can see below:
# Reporting Coordinates in MNI305 Space # Cluster Size(n) Size(mm^3) MNIX MNIY MNIZ Max# GRFCWP 1 200 1600.0 8.00 5.00 -17.00 -5.47411 0.00000 Unknown 2 59 472.0 34.00 -109.00 -19.00 -4.95360 0.00230 Unknown 3 66 528.0 -68.00 -79.00 11.00 -4.06504 0.00078 Unknown 4 78 624.0 20.00 35.00 35.00 -3.72711 0.00013 Right-Cerebral-White-Matter
I am not sure if I am doing something wrong but is there a way that I can visualize this clusters with Freeview?
Many thanks, Antonella
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, December 5, 2011 11:53 AM *Subject:* Re: [Freesurfer] DTI analysis and mri_glmfit-sim \
Hi Antonella, are there any clusters listed in the summary file? It might be that you just don't have any clusters that survive. doug
Antonella Kis wrote:
Dear all:
I am doing an FA group study (controls vs. patients without any
covariant so my C = +1.00000 -1.00000) and I want to see if there are any clusters that survives by multiple comparison so I ran:
mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd DTI_group_analysis.fsgd --C contrast.mtx --glmdir
group_analysis.glmdir
and then:
mri_glmfit-sim \ --glmdir group_analysis.glmdir \ --grf 2 neg \ --cwpvalthresh .025 \ --overwrite
One of the output files is group_analysis.glmdir /contrast/sig.mgh
which by my understanding is the significant uncorrected map which I can visualize it using freeview:
freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-fa-tal.nii \
/media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh:colormap=heat
The significant and corrected map containing the surviving clusters
by multiple comparison should be the grf.th2.neg.sig.cluster.mgh file but unfortunately when I try to visualize this clusters with Freeview I cannot see anything.
Can you please give me an advise on how I can see this clusters over
the group-fa-tal.nii?
This is what I was trying and the only thing I can see is a white mask:
freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-fa-tal.nii \
/media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th2.neg.sig.cluster.mgh:colormap=heat
Am I doing something wrong?
Thank you for your time and help.
Antonella
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 Fax: 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
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.