Re: [Freesurfer] Different results in surface and volume analyses
Hi Doug, Thanks for the response. Is this masking out of the cortical regions in the volume analysis a newer aspect of the processing stream? Previously I have seen this activation in the volume. It would be great if you could let me know the flags to see the full volume analysis. Thanks! Emily Message: 41 Date: Wed, 07 Aug 2013 19:29:33 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Different results in surface and volume analyses To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5202d85d.1090...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Emily, the processing stream is designed to mask out cortical regions from the volume analysis. The volume analysis is used for subcortical structures. To make sure that the same voxels are not analyzed twice, the cortical surface is masked out of the mni305 analysis. doug ps. If you really want to see the full volume analysis, then there are some flags that will do this. Message: 14 Date: Wed, 7 Aug 2013 13:15:37 -0400 From: Emily Boeke eboek...@nmr.mgh.harvard.edu Subject: [Freesurfer] Different results in surface and volume analyses To: freesurfer@nmr.mgh.harvard.edu Message-ID: 948e8fdf-754a-4ae0-a0c9-86d848f14...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=us-ascii Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily ___ 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] Different results in surface and volume analyses
Run mri_preproc with the -no-subcort-mask option Before you do that, delete the mni305 files in your run directories, otherwise it will not regenerate them. doug On 08/08/2013 11:17 AM, Emily Boeke wrote: Hi Doug, Thanks for the response. Is this masking out of the cortical regions in the volume analysis a newer aspect of the processing stream? Previously I have seen this activation in the volume. It would be great if you could let me know the flags to see the full volume analysis. Thanks! Emily Message: 41 Date: Wed, 07 Aug 2013 19:29:33 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Different results in surface and volume analyses To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 5202d85d.1090...@nmr.mgh.harvard.edu mailto:5202d85d.1090...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Emily, the processing stream is designed to mask out cortical regions from the volume analysis. The volume analysis is used for subcortical structures. To make sure that the same voxels are not analyzed twice, the cortical surface is masked out of the mni305 analysis. doug ps. If you really want to see the full volume analysis, then there are some flags that will do this. Message: 14 Date: Wed, 7 Aug 2013 13:15:37 -0400 From: Emily Boeke eboek...@nmr.mgh.harvard.edu mailto:eboek...@nmr.mgh.harvard.edu Subject: [Freesurfer] Different results in surface and volume analyses To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 948e8fdf-754a-4ae0-a0c9-86d848f14...@nmr.mgh.harvard.edu mailto:948e8fdf-754a-4ae0-a0c9-86d848f14...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=us-ascii Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily ___ 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 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] Different results in surface and volume analyses
Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily ___ 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] Different results in surface and volume analyses
Hi Emily, the processing stream is designed to mask out cortical regions from the volume analysis. The volume analysis is used for subcortical structures. To make sure that the same voxels are not analyzed twice, the cortical surface is masked out of the mni305 analysis. doug ps. If you really want to see the full volume analysis, then there are some flags that will do this. On 08/07/2013 01:15 PM, Emily Boeke wrote: Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily ___ 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 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.
