On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve <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>> 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>
> > 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/
>
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> --
> 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