10 Feb
2016
10 Feb
'16
12:59 p.m.
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
10 Feb
10 Feb
1:41 p.m.
New subject: Permission denied error with mri_surfcluster command
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 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/
1:47 p.m.
New subject: Permission denied error with mri_surfcluster command
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 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 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.
--
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University
1:50 p.m.
New subject: Permission denied error with mri_surfcluster command
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/ _______________________________________________ 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/
5:11 p.m.
New subject: Permission denied error with mri_surfcluster command
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
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
11:04 p.m.
New subject: Permission denied error with mri_surfcluster command
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
11 Feb
11 Feb
11:19 a.m.
New subject: Permission denied error with mri_surfcluster command
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.
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?
Your help is greatly appreciated,
Jen
On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve 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> 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 stilleither
> 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
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
--
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University
11:39 a.m.
New subject: Permission denied error with mri_surfcluster command
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/
1:07 p.m.
New subject: Permission denied error with mri_surfcluster command
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
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/GroupAnalysisClusterSum...
?
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%3E.
> > 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/
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
1:32 p.m.
New subject: Permission denied error with mri_surfcluster command
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/
25 Feb
25 Feb
1:52 p.m.
New subject: Permission denied error with mri_surfcluster command
Hi Douglas,
Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the CSD file and I selected the fwhm01 csd file.
I then ran the mri_surfcluster command, however, I got the following error:
ERROR: you have specified srcsubjid=fsaverage on cmdline, but CSD file was created with fsaverage
Any suggestions you have would be appreciated.
Best,
Jen
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. Youwill
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. Seethe
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 inputfile,
>> 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/GroupAnalysisClusterSum...
? >> >> 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), howeverI
>> 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-runwith
>> --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 toyou
>> 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
1 Mar
1 Mar
3:27 p.m.
New subject: Permission denied error with mri_surfcluster command
can you send your command line and terminal output?
On 02/25/2016 01:52 PM, Jennifer Legault wrote:
Hi Douglas,
Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the CSD file and I selected the fwhm01 csd file.
I then ran the mri_surfcluster command, however, I got the following error:
ERROR: you have specified srcsubjid=fsaverage on cmdline, but CSD file was created with fsaverage
Any suggestions you have would be appreciated.
Best,
Jen
On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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> <mailto: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>> > <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: > > > > 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>> > <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: > >> > >> 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>>> > >> <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 <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>>> > >> > <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 <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>>> > >> <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 <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>>> > >> <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 <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>>> <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> > >> > > <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> > >> > > >> > <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>>> > >> <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 <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>> > >> <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>> > >> 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> > >> <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 > >> > >> > >> > >> > >> -- > >> 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 > > > > > > _______________________________________________ > > 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 > Fax: 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> > 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/
4:42 p.m.
New subject: Permission denied error with mri_surfcluster command
Hi Doug,
Thank you for responding. I actually realized what was the matter (I had specified the path for fsaverage which led to the error; this is no longer an issue so long as I use "--subject fsaverage" instead of "--subject /path/fsaverage."
Here is the command I've been running for mri_surfcluster:
mri_surfcluster --subject fsaverage --hemi rh --in /path/rh_time_spval.mgh --csd /usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd --cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --sign pos --o /path/rh_time_cluster_cwp0001.mgh --cwsig /path/rh_time_cluster_mni_cwp0001.mgh --sum /path/rh_time_cluster_mni_sum
I do consistently have an issue though where the final output seems to be inaccurate (even with CWP of p<.0001 and FDR correction, I receive over 800 significant clusters). I am assuming this is a problem with the LME multivariate analysis script, although I am not exactly sure which part of the script needs to be changed. Attached is a screenshot of the output (visualized with freeview), as well as the matlab script and the qdec file (with fsid, fsid-base, MRI (time), group, and eTIV as columns). This script is geared towards examining changes in the brain after cognitive training lasting 2-3 weeks. If you have the time to look over this and let me know of any recommendations you have, it would be greatly appreciated.
Best,
Jennifer Legault
On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send your command line and terminal output?
On 02/25/2016 01:52 PM, Jennifer Legault wrote:
Hi Douglas,
Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the CSD file and I selected the fwhm01 csd file.
I then ran the mri_surfcluster command, however, I got the following error:
ERROR: you have specified srcsubjid=fsaverage on cmdline, but CSD file was created with fsaverage
Any suggestions you have would be appreciated.
Best,
Jen
On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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> <mailto: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>> > <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: > > > > 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>> > <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: > >> > >> 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>>> > >> <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 <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>>> > >> > <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 <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>>> > >> <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 <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>>> > >> <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 <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>>> <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> > >> > > <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> > >> > > >> > <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>>> > >> <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 <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>> > >> <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>> > >> 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> > >> <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 > >> > >> > >> > >> > >> -- > >> 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 > > > > > > _______________________________________________ > > 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 > Fax: 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> > 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
3 Mar
3 Mar
12:24 p.m.
New subject: Permission denied error with mri_surfcluster command
Can you send me rh_time_spval.mgh?
On 03/01/2016 04:42 PM, Jennifer Legault wrote:
Hi Doug,
Thank you for responding. I actually realized what was the matter (I had specified the path for fsaverage which led to the error; this is no longer an issue so long as I use "--subject fsaverage" instead of "--subject /path/fsaverage."
Here is the command I've been running for mri_surfcluster:
mri_surfcluster --subject fsaverage --hemi rh --in /path/rh_time_spval.mgh --csd /usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd --cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --sign pos --o /path/rh_time_cluster_cwp0001.mgh --cwsig /path/rh_time_cluster_mni_cwp0001.mgh --sum /path/rh_time_cluster_mni_sum
I do consistently have an issue though where the final output seems to be inaccurate (even with CWP of p<.0001 and FDR correction, I receive over 800 significant clusters). I am assuming this is a problem with the LME multivariate analysis script, although I am not exactly sure which part of the script needs to be changed. Attached is a screenshot of the output (visualized with freeview), as well as the matlab script and the qdec file (with fsid, fsid-base, MRI (time), group, and eTIV as columns). This script is geared towards examining changes in the brain after cognitive training lasting 2-3 weeks. If you have the time to look over this and let me know of any recommendations you have, it would be greatly appreciated.
Best,
Jennifer Legault
On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send your command line and terminal output?
On 02/25/2016 01:52 PM, Jennifer Legault wrote:
Hi Douglas,
Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the CSD file and I selected the fwhm01 csd file.
I then ran the mri_surfcluster command, however, I got the following error:
ERROR: you have specified srcsubjid=fsaverage on cmdline, but CSD file was created with fsaverage
Any suggestions you have would be appreciated.
Best,
Jen
On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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> <mailto: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>> > <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: > > > > 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>> > <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: > >> > >> 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>>> > >> <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 <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>>> > >> > <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 <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>>> > >> <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 <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>>> > >> <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 <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>>> <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> > >> > > <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> > >> > > >> > <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>>> > >> <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 <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>> > >> <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>> > >> 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> > >> <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 > >> > >> > >> > >> > >> -- > >> 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 > > > > > > _______________________________________________ > > 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 > Fax: 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> > 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
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/
12:34 p.m.
New subject: Permission denied error with mri_surfcluster command
Absolutely, here it is attached. Thank you for looking into this.
Best,
Jen
On Thu, Mar 3, 2016 at 12:24 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you send me rh_time_spval.mgh?
On 03/01/2016 04:42 PM, Jennifer Legault wrote:
Hi Doug,
Thank you for responding. I actually realized what was the matter (I had specified the path for fsaverage which led to the error; this is no longer an issue so long as I use "--subject fsaverage" instead of "--subject /path/fsaverage."
Here is the command I've been running for mri_surfcluster:
mri_surfcluster --subject fsaverage --hemi rh --in /path/rh_time_spval.mgh --csd
/usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd
--cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --sign pos --o /path/rh_time_cluster_cwp0001.mgh --cwsig /path/rh_time_cluster_mni_cwp0001.mgh --sum /path/rh_time_cluster_mni_sum
I do consistently have an issue though where the final output seems to be inaccurate (even with CWP of p<.0001 and FDR correction, I receive over 800 significant clusters). I am assuming this is a problem with the LME multivariate analysis script, although I am not exactly sure which part of the script needs to be changed. Attached is a screenshot of the output (visualized with freeview), as well as the matlab script and the qdec file (with fsid, fsid-base, MRI (time), group, and eTIV as columns). This script is geared towards examining changes in the brain after cognitive training lasting 2-3 weeks. If you have the time to look over this and let me know of any recommendations you have, it would be greatly appreciated.
Best,
Jennifer Legault
On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send your command line and terminal output?
On 02/25/2016 01:52 PM, Jennifer Legault wrote:
Hi Douglas,
Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the CSD file and I selected the fwhm01 csd file.
I then ran the mri_surfcluster command, however, I got the following error:
ERROR: you have specified srcsubjid=fsaverage on cmdline, but CSD file was created with fsaverage
Any suggestions you have would be appreciated.
Best,
Jen
On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
by "volume" do you mean a VBM-type analysis or do you mean thevolume
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 previouslyinstructed
> 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 thevoxel-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 onlyoutputs
> are a summary file and a .w file, and freeview doesn't acceptthis
> format. Is it possible to have a cluster-wise corrected map (a > sig.cluster.mgh file) as they do for the Clusterwise Correctionfor
> Multiple Comparisons tutorial here > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis%3E?
> > > 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> <mailto: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 theglm_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>>
> <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: > > > > 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 itwith
> --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 Iadd 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/GroupAnalysisClusterSum...
?
> >> > >> 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>>
> <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: > >> > >> 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 NGreve
> >> > <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>>> > >> <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 <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > >> > > >> > Try specifying the full path to the output > >> > > >> > On 02/10/2016 12:59 PM, Jennifer Legaultwrote:
> >> > > 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%3E.
> >> > > 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 thispatch
> >> > > > >> > > >> > <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 =
> >> > > overall max = 1 at vertex 27 > >> > > overall min = 1.52021e-05 at vertex125620
> >> > > 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 torh_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>>> > >> > <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 <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>>> > >> <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 <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>>> > >> <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 <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>>> <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> > >> > > <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%3E
> >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
> >> > > >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
> >> > 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>>> > >> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > The information in this e-mail is intendedonly
> 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 . Ifthe
> 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>> > >> <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>> > >> 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> > >> <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%3E
> >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
> >> 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
> >> > >> > >> > >> > >> -- > >> 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
> > > > > > _______________________________________________ > > 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 forthe
> person to > > whom it is > > addressed. If you believe this e-mail was sent to youin
> error and > > the e-mail > > contains patient information, please contact thePartners
> > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mailwas
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 > Fax: 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%3E
> 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> > 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
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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
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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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--
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University
12:39 p.m.
New subject: Permission denied error with mri_surfcluster command
All the values are between 0 and 1, so I suspect this is a map of p-values, not a map of -log10(p). Is that right? If so, convert it to -log10(p) and rerun. You can do this in matlab with p = MRIread('rh_time.mgh'); sig = p; sig.vol = -log10(abs(p.vol)); MRIwrite(sig,'sig.mgh');
On 03/03/2016 12:34 PM, Jennifer Legault wrote:
Absolutely, here it is attached. Thank you for looking into this.
Best,
Jen
On Thu, Mar 3, 2016 at 12:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send me rh_time_spval.mgh? On 03/01/2016 04:42 PM, Jennifer Legault wrote: > Hi Doug, > > Thank you for responding. I actually realized what was the matter (I > had specified the path for fsaverage which led to the error; this is > no longer an issue so long as I use "--subject fsaverage" instead of > "--subject /path/fsaverage." > > Here is the command I've been running for mri_surfcluster: > > mri_surfcluster --subject fsaverage --hemi rh --in > /path/rh_time_spval.mgh --csd > /usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd > --cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --sign pos > --o /path/rh_time_cluster_cwp0001.mgh --cwsig > /path/rh_time_cluster_mni_cwp0001.mgh --sum > /path/rh_time_cluster_mni_sum > > > I do consistently have an issue though where the final output seems to > be inaccurate (even with CWP of p<.0001 and FDR correction, I receive > over 800 significant clusters). I am assuming this is a problem with > the LME multivariate analysis script, although I am not exactly sure > which part of the script needs to be changed. Attached is a > screenshot of the output (visualized with freeview), as well as the > matlab script and the qdec file (with fsid, fsid-base, MRI (time), > group, and eTIV as columns). This script is geared towards examining > changes in the brain after cognitive training lasting 2-3 weeks. If > you have the time to look over this and let me know of any > recommendations you have, it would be greatly appreciated. > > Best, > > Jennifer Legault > > On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> can you send your command line and terminal output? >> >> On 02/25/2016 01:52 PM, Jennifer Legault wrote: >>> Hi Douglas, >>> >>> Thank you for all your help. When I say "volume" I do mean the FS >>> thickness*area measure. I ran the mri_glmfit with --osgm and for the >>> FWHM received the value of .925737. Assuming that this rounds up to 1, >>> I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to >>> find the CSD file and I selected the fwhm01 csd file. >>> >>> I then ran the mri_surfcluster command, however, I got the following >>> error: >>> >>> ERROR: you have specified srcsubjid=fsaverage on cmdline, but >>> CSD file was created with fsaverage >>> >>> Any suggestions you have would be appreciated. >>> >>> Best, >>> >>> Jen >>> >>> On Thu, Feb 11, 2016 at 1:32 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: >>> >>> 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> <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: >>> > >>> > >>> > >>> > 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>> >>> <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 <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: >>> > > >>> > > 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>> >>> <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 <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: >>> > >> >>> > >> 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>>> >>> > >> <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 <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> >>> <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 <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>>> >>> > >> <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 <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> >>> <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 <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>>> >>> > >> <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 <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> >>> <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 <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>>> >>> > <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 <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> <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>>> <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> >>> > >> >>> <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> >>> > >> >>> > <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>>> >>> > >> <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 <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> >>> <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 <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>> >>> > <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 <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>>> >>> > <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 <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> >>> > <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> >>> > >> >>> > <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>>> >>> > >> <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 <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>> >>> > <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 <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 >>> > > >>> > > >>> > > _______________________________________________ >>> > > 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>>> >>> > <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 <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>> >>> > <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 >>> > Fax: 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 >>> > >>> > >>> > >>> > >>> > -- >>> > 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 >>> Fax: 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> >>> 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 > > > > > _______________________________________________ > 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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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4 Mar
4 Mar
11:29 a.m.
New subject: Permission denied error with mri_surfcluster command
Thank you so much! Yes you are correct in that the map was initially of p-values and now I have changed it, and ran the mri_surfcluster command, the output looks much more reasonable (4 significant clusters as compared to the previous >800).
I was wondering, to visualize and cluster threshold the subcortical (segmented) data, does it make more sense to use mri_volcluster? Or can I use mri_surfcluster and use some argument to call up the aseg atlas instead of the annot -aparc argument?
I sincerely appreciate all your help.
Best,
Jen
On Thu, Mar 3, 2016 at 12:39 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
All the values are between 0 and 1, so I suspect this is a map of p-values, not a map of -log10(p). Is that right? If so, convert it to -log10(p) and rerun. You can do this in matlab with p = MRIread('rh_time.mgh'); sig = p; sig.vol = -log10(abs(p.vol)); MRIwrite(sig,'sig.mgh');
On 03/03/2016 12:34 PM, Jennifer Legault wrote:
Absolutely, here it is attached. Thank you for looking into this.
Best,
Jen
On Thu, Mar 3, 2016 at 12:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send me rh_time_spval.mgh? On 03/01/2016 04:42 PM, Jennifer Legault wrote: > Hi Doug, > > Thank you for responding. I actually realized what was the matter (I > had specified the path for fsaverage which led to the error; thisis
> no longer an issue so long as I use "--subject fsaverage" insteadof
> "--subject /path/fsaverage." > > Here is the command I've been running for mri_surfcluster: > > mri_surfcluster --subject fsaverage --hemi rh --in > /path/rh_time_spval.mgh --csd >/usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd
> --cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --signpos
> --o /path/rh_time_cluster_cwp0001.mgh --cwsig > /path/rh_time_cluster_mni_cwp0001.mgh --sum > /path/rh_time_cluster_mni_sum > > > I do consistently have an issue though where the final output seems to > be inaccurate (even with CWP of p<.0001 and FDR correction, I receive > over 800 significant clusters). I am assuming this is a problem with > the LME multivariate analysis script, although I am not exactlysure
> which part of the script needs to be changed. Attached is a > screenshot of the output (visualized with freeview), as well as the > matlab script and the qdec file (with fsid, fsid-base, MRI (time), > group, and eTIV as columns). This script is geared towards examining > changes in the brain after cognitive training lasting 2-3 weeks.If
> you have the time to look over this and let me know of any > recommendations you have, it would be greatly appreciated. > > Best, > > Jennifer Legault > > On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> can you send your command line and terminal output? >> >> On 02/25/2016 01:52 PM, Jennifer Legault wrote: >>> Hi Douglas, >>> >>> Thank you for all your help. When I say "volume" I do mean theFS
>>> thickness*area measure. I ran the mri_glmfit with --osgm and for the >>> FWHM received the value of .925737. Assuming that this rounds up to 1, >>> I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverageto
>>> find the CSD file and I selected the fwhm01 csd file. >>> >>> I then ran the mri_surfcluster command, however, I got the following >>> error: >>> >>> ERROR: you have specified srcsubjid=fsaverage on cmdline, but >>> CSD file was created with fsaverage >>> >>> Any suggestions you have would be appreciated. >>> >>> Best, >>> >>> Jen >>> >>> On Thu, Feb 11, 2016 at 1:32 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: >>> >>> 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 .wfile
>>> >>> >>> 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 thinkit
>>> 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 <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: >>> > >>> > >>> > >>> > 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>> >>> <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 <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: >>> > > >>> > > There is a (very long) command line on that page. Mainly you >>> > need >>> > > a csd file. To get that you need the FWHM ofyour
>>> 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/GroupAnalysisClusterSum...
? >>> > >> >>> > >> 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>> >>> <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 <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: >>> > >> >>> > >> 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>>> >>> > >> <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 <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> >>> <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 <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 thepermission
>>> is denied. >>> > >> > > >>> > >> > > This is the command I am trying torun:
>>> > >> > > >>> > >> > > 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>>> >>> > >> <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 <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> >>> <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 <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>>> >>> > >> <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 <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> >>> <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 <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>>> >>> > <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 <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> <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>>> <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%3E
>>> > >> >>> <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%3E
>>> > <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>>> >>> > >> <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 <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> >>> <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 <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-mailwas
>>> 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>> >>> > <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 <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>>> > <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 <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> >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%3E
>>> > >> >>> <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%3E
>>> > <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>>> >>> > >> <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 <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>> >>> > <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 <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 >>> > > >>> > > >>> > > _______________________________________________ >>> > > 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>>> >>> > <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 <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>> >>> > <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 >>> > Fax: 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%3E
>>> > 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%3E
>>> > <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 >>> > >>> > >>> > >>> > >>> > -- >>> > 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 >>> Fax: 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%3E
>>> 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> >>> 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 > > > > > _______________________________________________ > 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
3742
Age (days ago)
3765
Last active (days ago)
freesurfer@nmr.mgh.harvard.edu
16 comments
3 participants
participants (3)
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Douglas Greve -
Douglas N Greve
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Jennifer Legault