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
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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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: 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.
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.
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Douglas N Greve