On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

by "volume" do you mean a VBM-type analysis or do you mean the volume
that comes out of FS (thickness*area)? If you are going to use a
clusterwise correction, then you have to have a FWHM measurement. You
can try analyzing it in mri_glmfit with --osgm just to get the FWHM out
of it.

You should be able to output a .mgh file instead of a .w file

On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> That's very useful, thank you. In terms of FWHM, I am examining gray
> matter volume, not cortical thickness, and was previously instructed
> by Martin Reuter not to smooth these data. Do you think it would make
> sense then to just use the fwhm01? And in terms of the voxel-wise
> threshold, is there a commonly used value for GM volume data? I am
> still new to freesurfer and I appreciate any feedback.
>
> For visualization, after I run the mri_surfcluster the only outputs
> are a summary file and a .w file, and freeview doesn't accept this
> format. Is it possible to have a cluster-wise corrected map (a
> sig.cluster.mgh file) as they do for the Clusterwise Correction for
> Multiple Comparisons tutorial here
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>?
>
>
> Best,
>
> Jen
>
> On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>
> On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > Thank you for your response. Do I need to run the glm_fit-sim
> command
> > to make the csd file? I feel this would be inappropriate for my
> data
> > since I already ran the LME model.
> No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
> need the FWHM though
> >
> > Second, is there an argument to make an output file that can be
> > visualized via freeview? In other words, how can I view my cluster
> > thresholded data?
> You can use freeview, something like
> freeview -f lh.inflated:overlay=sig.mgh
> There are other options for loading annotations and curvature. See the
> freeview help
> >
> > Your help is greatly appreciated,
> >
> > Jen
> >
> >
> >
> > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > There is a (very long) command line on that page. Mainly you
> need
> > a csd file. To get that you need the FWHM of your analysis, the
> > voxel-wise threshold, and the sign of the contrast (or abs).
> Then
> > the relevant output will be the --sum. You can run it with
> --help
> > to get more info.
> >
> >
> > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> >> Thank you very much for your help! I still received a "cannot
> >> read file type" error when I only added the path to the output
> >> --o part, however when I also added the path to the input file,
> >> it worked!
> >>
> >> I do have one more question: Which argument can I add so
> that in
> >> my output file I see the clusterwise P value, like it is shown
> >> here
> >>
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary>?
> >>
> >> Best,
> >>
> >> Jen
> >>
> >> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
> >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >>
> >> I meant for the output files, so the --o in particular
> >>
> >> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> >> > Douglas,
> >> >
> >> > Thank you for your quick response. When I add --sd
> >> [path_location], I
> >> > get the following error:
> >> > Loading source values
> >> > mri_read(): couldn't determine type of file
> >> [path_location]/rh_time_spval
> >> > ERROR: could not read rh_time_spval as type
> >> >
> >> > Should I use another argument?
> >> >
> >> > Best,
> >> >
> >> > Jen
> >> >
> >> >
> >> >
> >> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
> >> > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> >> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> >> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> >> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> >> >
> >> > Try specifying the full path to the output
> >> >
> >> > On 02/10/2016 12:59 PM, Jennifer Legault wrote:
> >> > > Dear experts,
> >> > >
> >> > > I am trying to use the cluster thresholding command
> >> for my
> >> > freesurfer
> >> > > LME outputs as referred to here
> >> > >
> >> >
> >>
> <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels>.
> >> > > Any feedback or comments would be greatly
> appreciated.
> >> > >
> >> > > I am aware that there have been permission denied
> >> errors when using
> >> > > mri_surfcluster and that applying this patch
> >> > >
> >> >
> >>
> <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg>
> >> > > should solve the problem (which I tried), however I
> >> am still either
> >> > > receiving errors stating the permission is denied.
> >> > >
> >> > > This is the command I am trying to run:
> >> > >
> >> > > mri_surfcluster --subject fsaverage --hemi rh --in
> >> > rh_time_spval.mgh
> >> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o
> >> rh_time_cluster --sum
> >> > > rh_time_cluster_sum
> >> > >
> >> > >
> >> > > Here is the error log:
> >> > >
> >> > > mri_surfcluster --subject fsaverage --hemi rh --in
> >> rh_time_spval.mgh
> >> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o
> >> rh_time_cluster --sum
> >> > > rh_time_cluster_sum thsign = pos, id = 1
> >> > > version $Id: mri_surfcluster.c,v 1.51.2.3
> 2012/05/31
> >> 22:10:05
> >> > greve Exp $
> >> > > hemi = rh
> >> > > srcid = rh_time_spval.mgh
> >> > > srcsubjid = fsaverage
> >> > > srcsurf = white
> >> > > srcframe = 0
> >> > > thsign = pos
> >> > > thmin = -1
> >> > > thmax = -1
> >> > > fdr = 0.05
> >> > > minarea = 0
> >> > > xfmfile = talairach.xfm
> >> > > nth = -1
> >> > > outid = rh_time_cluster paint
> >> > > sumfile = rh_time_cluster_sum
> >> > > subjectsdir = /gpfs/home/jtl190/work/structurals
> >> > > FixMNI = 1
> >> > > ------------- XFM matrix (RAS2RAS) ---------------
> >> > >
> >> >
> >>
> /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
> >> > > 1.000 0.000 0.000 0.000;
> >> > > 0.000 1.000 0.000 0.000;
> >> > > 0.000 0.000 1.000 0.000;
> >> > > 0.000 0.000 0.000 1.000;
> >> > >
> ----------------------------------------------------
> >> > > Reading source surface
> >> > >
> >> /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
> >> > > Done reading source surface
> >> > > Computing metric properties
> >> > > Loading source values
> >> > > number of voxels in search space = 163842
> >> > > Done loading source values (nvtxs = 163842)
> >> > > overall max = 1 at vertex 27
> >> > > overall min = 1.52021e-05 at vertex 125620
> >> > > surface nvertices 163842
> >> > > surface area 65020.929688
> >> > > surface area 65020.765625
> >> > > Setting voxel-wise threshold with FDR = 0.050000
> >> > > Assuming input map is -log10(p)
> >> > > MRISfdr2vwth(): np = 163842, nv = 163842, fdr =
> 0.05,
> >> vwth=1.04576
> >> > > FDR Voxel-wise threshold is 1.04576
> >> > > Adjusting threshold for 1-tailed test.
> >> > > If the input is not a -log10(p) volume, re-run with
> >> --no-adjust.
> >> > > Searching for Clusters ...
> >> > > thmin=1.045757 (0.744727), thmax=-1.000000 (-1),
> >> thsignid=1,
> >> > > minarea=0.000000
> >> > > Found 9803 clusters
> >> > > Max cluster size 5993.586426
> >> > > INFO: fixing MNI talairach coordinates
> >> > > Saving thresholded output to rh_time_cluster
> >> > > Can't create file
> >> > >
> >> >
> >>
> /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w
> >> > >
> >> > > Permission denied
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > Thank you for taking the time to read this email.
> >> > >
> >> > > Sincerely,
> >> > >
> >> > > Jennifer Legault
> >> > >
> >> > > --
> >> > > Jennifer Legault
> >> > > Ph.D candidate, Neuroscience
> >> > > Brain, Language, and Computation Lab
> >> > > The Pennsylvania State University
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > Freesurfer mailing list
> >> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> <mailto: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>
> >> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> >> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>

> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> >> > Phone Number: 617-724-2358 <tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358>>
> >> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
> <tel:617-724-2358>>>
> >> > Fax: 617-726-7422 <tel:617-726-7422>
> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
> <tel:617-726-7422>
> >> <tel:617-726-7422 <tel:617-726-7422>>>
> >> >
> >> > Bugs:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> >> >
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> >> > FileDrop: 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>
> >>
> <http://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/
> >> >
> >> > _______________________________________________
> >> > Freesurfer mailing list
> >> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu

> <mailto: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.
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > Jennifer Legault
> >> > Ph.D candidate, Neuroscience
> >> > Brain, Language, and Computation Lab
> >> > The Pennsylvania State University
> >> >
> >> >
> >> > _______________________________________________
> >> > Freesurfer mailing list
> >> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> <mailto: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>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> >> Phone Number: 617-724-2358 <tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358>>
> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> <tel:617-726-7422>>
> >>
> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> >> FileDrop: 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>
> >>
> <http://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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
> >>

> >> --
> >> Jennifer Legault
> >> Ph.D candidate, Neuroscience
> >> Brain, Language, and Computation Lab
> >> The Pennsylvania State University
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >

> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto: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.
> >
> >
> >
> >
> > --
> > Jennifer Legault
> > Ph.D candidate, Neuroscience
> > Brain, Language, and Computation Lab
> > The Pennsylvania State University
> >
> >
> > _______________________________________________
> > 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: 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/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> --
> Jennifer Legault
> Ph.D candidate, Neuroscience
> Brain, Language, and Computation Lab
> The Pennsylvania State University
>
>
> _______________________________________________
> 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

Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University