Re: [Freesurfer] Abblocked Setup
Chindhuri Selvadurai wrote: Dear Doug, Thanks for your response! Our stimuli starts with the null condition, but abblocked assumes it's the ON condition. Is there a way to invert this? No, not currently, though you can tell tkmedit/tksurfer to invert the color scale. Or you can do it by hand by multiplying the image by -1 (with fscalc). When we look at the sig maps, how do we know what the contrast is? Which condition does it think is null/task, negative/positive? From what I understand from your first e-mail, this is the opposite of what we want. I tried looking at the surface-based analysis using tksurfer, but since there is no constrast file for abblocked, I specified all contrasts, but how do you differentiate if you have more than one? tksurfer-sess -s PBMST08 -hemi -lh -analysis mandy_mst_v_mct_lh -call You can just specify -c fund etc. doug I think perhaps it would be better for us to switch to the block design to make things simpler? Thanks!! Chindhuri sfa-sess is depricated now (should not even be in there). Use selxavg3-sess. doug Chindhuri Selvadurai wrote: Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list
Re: [Freesurfer] Abblocked Setup
Dear Doug, Thanks for your response! Our stimuli starts with the null condition, but abblocked assumes it's the ON condition. Is there a way to invert this? When we look at the sig maps, how do we know what the contrast is? Which condition does it think is null/task, negative/positive? From what I understand from your first e-mail, this is the opposite of what we want. I tried looking at the surface-based analysis using tksurfer, but since there is no constrast file for abblocked, I specified all contrasts, but how do you differentiate if you have more than one? tksurfer-sess -s PBMST08 -hemi -lh -analysis mandy_mst_v_mct_lh -call I think perhaps it would be better for us to switch to the block design to make things simpler? Thanks!! Chindhuri sfa-sess is depricated now (should not even be in there). Use selxavg3-sess. doug Chindhuri Selvadurai wrote: Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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] Abblocked Setup
The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] abblocked Setup
Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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] Abblocked Setup
Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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] Abblocked Setup
sfa-sess is depricated now (should not even be in there). Use selxavg3-sess. doug Chindhuri Selvadurai wrote: Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
