Hi,
I was wondering if there is a way to perform fdr correction using command line in freesurfer without using matlab as mri_glmfit-sim only does bonferroni ?
Thanks Regards MV
Hi again.
I think I can obtain fdr maps by: mri_surfcluster --in sig.mgh --subject fsaverage --hemi lh --annot aparc --sign pos --o fdr_005_lh_pos.mgh --fdr 0.05 --cortex --mask mask.mgh
Can anyone comment if the above command is right to generate a clusterwise fdr corrected p<0.05?
Thanks
Regards
MV
On Fri, Oct 7, 2016 at 1:11 PM, neuroimage analyst < neuroimage.analyst@gmail.com> wrote:
Hi,
I was wondering if there is a way to perform fdr correction using command line in freesurfer without using matlab as mri_glmfit-sim only does bonferroni ?
Thanks Regards MV
try this binary
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr
On 10/07/2016 04:11 PM, neuroimage analyst wrote:
Hi,
I was wondering if there is a way to perform fdr correction using command line in freesurfer without using matlab as mri_glmfit-sim only does bonferroni ?
Thanks Regards MV
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Doug for the binary.
A quick follow-up: what does the sign in either mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are only positive and p-values obtained from them has sign of +/-. My understanding is + indicates where mean_A>mean_B and vice versa.
If for example, I am interested in mean_A>mean_B then should I pass --pos (mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected cluster defining threshold of p<0.005) in the contrast that was designed for that test?
Regards
MV
On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
try this binary
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr
On 10/07/2016 04:11 PM, neuroimage analyst wrote:
Hi,
I was wondering if there is a way to perform fdr correction using command line in freesurfer without using matlab as mri_glmfit-sim only does bonferroni ?
Thanks Regards MV
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: 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
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.
The sign depends on how you set up the contrast. If you are using an FSGD file and have two classes A and B and a contrast [+1 -1], then positive indicates A>B. The F.mgh is the map of F values which are unsigned. The gamma.mgh file will have the contrast values themselves including sign. The sig.mgh will be the -log10(p) signed by the sign of gamma.mgh at that vertex
On 10/12/2016 02:23 PM, neuroimage analyst wrote:
Thanks, Doug for the binary.
A quick follow-up: what does the sign in either mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are only positive and p-values obtained from them has sign of +/-. My understanding is + indicates where mean_A>mean_B and vice versa.
If for example, I am interested in mean_A>mean_B then should I pass --pos (mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected cluster defining threshold of p<0.005) in the contrast that was designed for that test?
Regards
MV
On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
try this binary https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr> On 10/07/2016 04:11 PM, neuroimage analyst wrote: > > Hi, > > I was wondering if there is a way to perform fdr correction using > command line in freesurfer without using matlab as mri_glmfit-sim only > does bonferroni ? > > Thanks > Regards > MV > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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/ <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 <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 <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
Thank you for that clarification,Doug.
VM
On Oct 12, 2016 12:09 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
The sign depends on how you set up the contrast. If you are using an FSGD file and have two classes A and B and a contrast [+1 -1], then positive indicates A>B. The F.mgh is the map of F values which are unsigned. The gamma.mgh file will have the contrast values themselves including sign. The sig.mgh will be the -log10(p) signed by the sign of gamma.mgh at that vertex
On 10/12/2016 02:23 PM, neuroimage analyst wrote:
Thanks, Doug for the binary.
A quick follow-up: what does the sign in either mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are only positive and p-values obtained from them has sign of +/-. My understanding is + indicates where mean_A>mean_B and vice versa.
If for example, I am interested in mean_A>mean_B then should I pass --pos (mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected cluster defining threshold of p<0.005) in the contrast that was designed for that test?
Regards
MV
On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
try this binary https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr> On 10/07/2016 04:11 PM, neuroimage analyst wrote: > > Hi, > > I was wondering if there is a way to perform fdr correction using > command line in freesurfer without using matlab as mri_glmfit-sim only > does bonferroni ? > > Thanks > Regards > MV > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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/ <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 <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 <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
-- 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
neuroimage analyst