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?


Best,

Jen

On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve <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>> 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>> 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>>> 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>>
>>         >     >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
>>         >
>>         >
>>         >     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 <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
>>         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
>>     <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>
>     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
> 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/

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