Hello all,
I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-values?
mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum cache.uncorr.abs.sig.ocn.dat
Thanks
corinna
Hi all, just following up on my previous question. For the purposes of showing uncorrected p-values <0.005 as well as the corrected results (via mri_glmfit-sim) I would like to get the table of uncorrected p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir --cache 2.3 abs --cwp 1 --2spaces and it does output p-values, but there has gone through the simulations. I would like the raw p-values from this step: mri_glmfit --y rh.noreg.thickness.08B.mgh --fsgd file.fsgd dods --C diff_noreg.mtx --surf fsaverage rh --cortex --glmdir rh.thick.noreg.sm08.glmdir
What command would I use?
Thanks Corinna
On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer corinnab83@gmail.com wrote:
Hello all,
I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-values?
mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum cache.uncorr.abs.sig.ocn.dat
Thanks
corinna
In the table produced by glmfit-sim, the maximum vertex-wise uncorrected -log10(p) is given. Is that enough?
On 10/03/2016 02:55 PM, Corinna Bauer wrote:
Hi all, just following up on my previous question. For the purposes of showing uncorrected p-values <0.005 as well as the corrected results (via mri_glmfit-sim) I would like to get the table of uncorrected p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir --cache 2.3 abs --cwp 1 --2spaces and it does output p-values, but there has gone through the simulations. I would like the raw p-values from this step: mri_glmfit --y rh.noreg.thickness.08B.mgh --fsgd file.fsgd dods --C diff_noreg.mtx --surf fsaverage rh --cortex --glmdir rh.thick.noreg.sm08.glmdir
What command would I use?
Thanks Corinna
On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer <corinnab83@gmail.com mailto:corinnab83@gmail.com> wrote:
Hello all, I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-values? mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum cache.uncorr.abs.sig.ocn.dat Thanks corinna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Should be, so long as it is the uncorrected value. Is that the CWPmax?
On Mon, Oct 3, 2016 at 2:57 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
In the table produced by glmfit-sim, the maximum vertex-wise uncorrected -log10(p) is given. Is that enough?
On 10/03/2016 02:55 PM, Corinna Bauer wrote:
Hi all, just following up on my previous question. For the purposes of showing uncorrected p-values <0.005 as well as the corrected results (via mri_glmfit-sim) I would like to get the table of uncorrected p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir --cache 2.3 abs --cwp 1 --2spaces and it does output p-values, but there has gone through the simulations. I would like the raw p-values from this step: mri_glmfit --y rh.noreg.thickness.08B.mgh --fsgd file.fsgd dods --C diff_noreg.mtx --surf fsaverage rh --cortex --glmdir rh.thick.noreg.sm08.glmdir
What command would I use?
Thanks Corinna
On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer <corinnab83@gmail.com mailto:corinnab83@gmail.com> wrote:
Hello all, I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-values? mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum cache.uncorr.abs.sig.ocn.dat Thanks corinna
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.
No, it is labeled as "Max", the 2nd column of the table. The next column is the VtxMax, the vertex where the max uncorrected appeared
On 10/03/2016 05:43 PM, Corinna Bauer wrote:
Should be, so long as it is the uncorrected value. Is that the CWPmax?
On Mon, Oct 3, 2016 at 2:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
In the table produced by glmfit-sim, the maximum vertex-wise uncorrected -log10(p) is given. Is that enough? On 10/03/2016 02:55 PM, Corinna Bauer wrote: > Hi all, just following up on my previous question. For the purposes of > showing uncorrected p-values <0.005 as well as the corrected results > (via mri_glmfit-sim) I would like to get the table of uncorrected > p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir > --cache 2.3 abs --cwp 1 --2spaces and it does output p-values, but > there has gone through the simulations. I would like the raw p-values > from this step: mri_glmfit --y rh.noreg.thickness.08B.mgh --fsgd > file.fsgd dods --C diff_noreg.mtx --surf fsaverage rh --cortex > --glmdir rh.thick.noreg.sm08.glmdir > > What command would I use? > > Thanks > Corinna > > > On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer <corinnab83@gmail.com <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com>>> wrote: > > Hello all, > > I would like to get a table of the uncorrected p-values to compare > with the corrected ones obtained using mri_glmfit-sim. I tried the > following, which outputs a table of clusters and their vertices, > but it does not include p-values. Is there a flag that I shoudl > include to output the p-values? > > mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi > lh --surf white --annot aparc --no-adjust --bonferroni 2 > --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot > cache.uncorr.abs.sig.ocn.annot --cwsig > cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum > cache.uncorr.abs.sig.ocn.dat > > Thanks > > corinna > > > > > _______________________________________________ > 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
freesurfer@nmr.mgh.harvard.edu
-
Corinna Bauer -
Douglas N Greve