Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
For some reason the spatial fwhm calculation is failing. This sometimes happens if the mask is highly fractured. Can you look at group.glm/mask.nii.gz and see if there are a bunch of isolated voxels? On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote: Hi Doug, Thanks for your reply. This is the terminal output: [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh sysname Darwin hostname Eran-Harels-MacBook-Pro.local machine i386 user eiran FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz logyflag 0 usedti 0 labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir group.glm IllCondOK 0 ReScaleX 1 DoFFx 0 wFile cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory group.glm Loading y from /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz Saving design matrix to group.glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. Pruning voxels by thr: 0.00 Found 75351 voxels in mask Saving mask to group.glm/mask.nii.gz Reshaping mriglm-mask... search space = 36561.555889 DOF = 26 Starting fit and test Fit completed in 0.0542833 minutes Computing spatial AR1 on surface Residual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nan Writing results osgm maxvox sig=5.1359 F=31.1425 at index 47512 0 0seed=1425981217 mri_glmfit done Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh SURFACE: fsaverage lh log file is group.glm/cache.mri_glmfit-sim.log cd /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr /Applications/freesurfer/bin/mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Mar 4 20:55:33 IST 2015 Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 eiran setenv SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = nan ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd Any ideas? Thanks, Eiran Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 Date: Mon, 02 Mar 2015 14:17:39 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks, Eiran -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hi Doug,It seems ok, no isolated voxels.I attach it.Any other ideas?Thanks,Eiran On Friday, March 6, 2015 6:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: For some reason the spatial fwhm calculation is failing. This sometimes happens if the mask is highly fractured. Can you look at group.glm/mask.nii.gz and see if there are a bunch of isolated voxels? On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote: Hi Doug, Thanks for your reply. This is the terminal output: [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh sysname Darwin hostname Eran-Harels-MacBook-Pro.local machine i386 user eiran FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz logyflag 0 usedti 0 labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir group.glm IllCondOK 0 ReScaleX 1 DoFFx 0 wFile cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory group.glm Loading y from /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz Saving design matrix to group.glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. Pruning voxels by thr: 0.00 Found 75351 voxels in mask Saving mask to group.glm/mask.nii.gz Reshaping mriglm-mask... search space = 36561.555889 DOF = 26 Starting fit and test Fit completed in 0.0542833 minutes Computing spatial AR1 on surface Residual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nan Writing results osgm maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217 mri_glmfit done Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh SURFACE: fsaverage lh log file is group.glm/cache.mri_glmfit-sim.log cd /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr /Applications/freesurfer/bin/mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Mar 4 20:55:33 IST 2015 Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 eiran setenv SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = nan ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd Any ideas? Thanks, Eiran Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 Date: Mon, 02 Mar 2015 14:17:39 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks, Eiran -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
There appears to be a bug in the computation of the fwhm and it appears that I fixed the bug somewhere between 5.3 and now. I've put a new version of mri_glmfit here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit see if that works for you doug On 03/06/2015 12:38 PM, Douglas N Greve wrote: Can you upload the ces.nii.gz and cesvar.nii.gz files to our filedrop?f On 03/06/2015 12:23 PM, Eiran Vadim Harel wrote: Hi Doug, It seems ok, no isolated voxels. I attach it. Any other ideas? Thanks, Eiran On Friday, March 6, 2015 6:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: For some reason the spatial fwhm calculation is failing. This sometimes happens if the mask is highly fractured. Can you look at group.glm/mask.nii.gz and see if there are a bunch of isolated voxels? On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote: Hi Doug, Thanks for your reply. This is the terminal output: [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh sysname Darwin hostname Eran-Harels-MacBook-Pro.local machine i386 user eiran FixVertexAreaFlag = 1 UseMaskWithSmoothing1 OneSampleGroupMean 1 y /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz logyflag 0 usedti 0 labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir group.glm IllCondOK 0 ReScaleX 1 DoFFx 0 wFile cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory group.glm Loading y from /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz Saving design matrix to group.glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. Pruning voxels by thr: 0.00 Found 75351 voxels in mask Saving mask to group.glm/mask.nii.gz Reshaping mriglm-mask... search space = 36561.555889 DOF = 26 Starting fit and test Fit completed in 0.0542833 minutes Computing spatial AR1 on surface Residual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nan Writing results osgm maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217 mri_glmfit done Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh SURFACE: fsaverage lh log file is group.glm/cache.mri_glmfit-sim.log cd /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr /Applications/freesurfer/bin/mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Mar 4 20:55:33 IST 2015 Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 eiran setenv SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = nan ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd Any ideas? Thanks, Eiran Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 Date: Mon, 02 Mar 2015 14:17:39 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Can you upload the ces.nii.gz and cesvar.nii.gz files to our filedrop?f On 03/06/2015 12:23 PM, Eiran Vadim Harel wrote: Hi Doug, It seems ok, no isolated voxels. I attach it. Any other ideas? Thanks, Eiran On Friday, March 6, 2015 6:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: For some reason the spatial fwhm calculation is failing. This sometimes happens if the mask is highly fractured. Can you look at group.glm/mask.nii.gz and see if there are a bunch of isolated voxels? On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote: Hi Doug, Thanks for your reply. This is the terminal output: [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh sysname Darwin hostname Eran-Harels-MacBook-Pro.local machine i386 user eiran FixVertexAreaFlag = 1 UseMaskWithSmoothing1 OneSampleGroupMean 1 y /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz logyflag 0 usedti 0 labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir group.glm IllCondOK 0 ReScaleX 1 DoFFx 0 wFile cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory group.glm Loading y from /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz Saving design matrix to group.glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. Pruning voxels by thr: 0.00 Found 75351 voxels in mask Saving mask to group.glm/mask.nii.gz Reshaping mriglm-mask... search space = 36561.555889 DOF = 26 Starting fit and test Fit completed in 0.0542833 minutes Computing spatial AR1 on surface Residual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nan Writing results osgm maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217 mri_glmfit done Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh SURFACE: fsaverage lh log file is group.glm/cache.mri_glmfit-sim.log cd /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr /Applications/freesurfer/bin/mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Mar 4 20:55:33 IST 2015 Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 eiran setenv SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = nan ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd Any ideas? Thanks, Eiran Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 Date: Mon, 02 Mar 2015 14:17:39 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hi Doug,It is giving me this
error:[Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm
--nii.gz --surface fsaverage lh/Applications/freesurfer/bin/mri_glmfit: line 9:
syntax error near unexpected token `('/Applications/freesurfer/bin/mri_glmfit:
line 9: `ELF ?@@(?^@8 @,)@?88@8@@@ꨍꨍ `.?%
?ʍTT@T@DD??P?td?\?\?Q?t/lib64/ld-linux-x86-64.so.2GNUGNU?L?ьUF?6?'
Thanks,Eiran
On Friday, March 6, 2015 8:26 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
There appears to be a bug in the computation of the fwhm and it appears
that I fixed the bug somewhere between 5.3 and now. I've put a new
version of mri_glmfit here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
see if that works for you
doug
On 03/06/2015 12:38 PM, Douglas N Greve wrote:
Can you upload the ces.nii.gz and cesvar.nii.gz files to our filedrop?f
On 03/06/2015 12:23 PM, Eiran Vadim Harel wrote:
Hi Doug,
It seems ok, no isolated voxels.
I attach it.
Any other ideas?
Thanks,
Eiran
On Friday, March 6, 2015 6:22 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
For some reason the spatial fwhm calculation is failing. This sometimes
happens if the mask is highly fractured. Can you look at
group.glm/mask.nii.gz and see if there are a bunch of isolated voxels?
On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote:
Hi Doug,
Thanks for your reply.
This is the terminal output:
[Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
group.glm --nii.gz --surface fsaverage lh
Reading source surface
/Applications/freesurfer/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd
/Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr
cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
group.glm --nii.gz --surface fsaverage lh
sysname Darwin
hostname Eran-Harels-MacBook-Pro.local
machine i386
user eiran
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y
/Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz
logyflag 0
usedti 0
labelmask
/Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label
maskinv 0
glmdir group.glm
IllCondOK 0
ReScaleX 1
DoFFx 0
wFile cesvar.nii.gz
weightinv 1
weightsqrt 1
Creating output directory group.glm
Loading y from
/Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz
Saving design matrix to group.glm/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 149955 points in label.
Pruning voxels by thr: 0.00
Found 75351 voxels in mask
Saving mask to group.glm/mask.nii.gz
Reshaping mriglm-mask...
search space = 36561.555889
DOF = 26
Starting fit and test
Fit completed in 0.0542833 minutes
Computing spatial AR1 on surface
Residual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nan
Writing results
osgm
maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217
mri_glmfit done
Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166
cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm
--glmdir group.glm --nii.gz --surface fsaverage lh
SURFACE: fsaverage lh
log file is group.glm/cache.mri_glmfit-sim.log
cd
/applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir group.glm --cache 3 pos --cwpvalthresh .0166
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Wed Mar 4 20:55:33 IST 2015
Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version
10.8.0: Tue Jun 7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386
eiran
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
group.glm --nii.gz --surface fsaverage lh
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = nan
ERROR: cannot find
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd
Any ideas?
Thanks,
Eiran
Subject: Re: [Freesurfer] confirm
5db71d8d19a634948b059d302f95d798f665a638
Date: Mon, 02 Mar 2015 14:17:39 -0500
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd Any ideas? Thanks, Eiran Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 Date: Mon, 02 Mar 2015 14:17:39 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support 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 To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks, Eiran -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@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/ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 mailto: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 gr...@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 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.
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
, Eiran Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 Date: Mon, 02 Mar 2015 14:17:39 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support 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 To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks, Eiran -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@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/ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 mailto: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 gr...@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
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hi Doug,Thanks for your reply.This is the terminal output: [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lhReading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.whiteNumber of vertices 163842Number of faces 327680Total area 65416.648438AvgVtxArea 0.399267AvgVtxDist 0.721953StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $cwd /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nrcmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh sysname Darwinhostname Eran-Harels-MacBook-Pro.localmachine i386user eiranFixVertexAreaFlag = 1UseMaskWithSmoothing 1OneSampleGroupMean 1y /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gzlogyflag 0usedti 0labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.labelmaskinv 0glmdir group.glmIllCondOK 0ReScaleX 1DoFFx 0wFile cesvar.nii.gzweightinv 1weightsqrt 1Creating output directory group.glmLoading y from /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gzSaving design matrix to group.glm/Xg.datNormalized matrix condition is 1Matrix condition is 1Found 149955 points in label.Pruning voxels by thr: 0.00Found 75351 voxels in maskSaving mask to group.glm/mask.nii.gzReshaping mriglm-mask...search space = 36561.555889DOF = 26Starting fit and testFit completed in 0.0542833 minutesComputing spatial AR1 on surfaceResidual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nanWriting results osgm maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217mri_glmfit done Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lhSURFACE: fsaverage lhlog file is group.glm/cache.mri_glmfit-sim.log cd /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr/Applications/freesurfer/bin/mri_glmfit-sim--glmdir group.glm --cache 3 pos --cwpvalthresh .0166 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $Wed Mar 4 20:55:33 IST 2015Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386eiransetenv SUBJECTS_DIR /Applications/freesurfer/subjectsFREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line:cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh DoSim = 0UseCache = 1DoPoll = 0DoPBSubmit = 0DoBackground = 0DiagCluster = 0gd2mtx = dodsfwhm = nanERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd Any ideas?Thanks,Eiran Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 Date: Mon, 02 Mar 2015 14:17:39 -0500 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks, Eiran ___ 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.
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks, Eiran On Monday, February 23, 2015 10:37 AM, freesurfer-requ...@nmr.mgh.harvard.edu freesurfer-requ...@nmr.mgh.harvard.edu wrote: Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 79.177.55.71 for subscription of your email address, eiranha...@yahoo.com mailto:eiranha...@yahoo.com, to the freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/5db71d8d19a634948b059d302f95d798f665a638 Or include the following line -- and only the following line -- in a message to freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu: confirm 5db71d8d19a634948b059d302f95d798f665a638 Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional Re: text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-ow...@nmr.mgh.harvard.edu. mailto:freesurfer-ow...@nmr.mgh.harvard.edu. 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. ___ 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 gr...@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
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks,Eiran On Monday, February 23, 2015 10:37 AM, freesurfer-requ...@nmr.mgh.harvard.edu freesurfer-requ...@nmr.mgh.harvard.edu wrote: Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 79.177.55.71 for subscription of your email address, eiranha...@yahoo.com, to the freesurfer@nmr.mgh.harvard.edu mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/5db71d8d19a634948b059d302f95d798f665a638 Or include the following line -- and only the following line -- in a message to freesurfer-requ...@nmr.mgh.harvard.edu: confirm 5db71d8d19a634948b059d302f95d798f665a638 Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional Re: text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-ow...@nmr.mgh.harvard.edu. 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. ___ 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.
