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 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 --inrh_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/ _______________________________________________ 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
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-- 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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