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 <gr...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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: 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.
_______________________________________________
Freesurfer mailing list
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.
