Re: [Freesurfer] mris_preproc with --xhemi
By real I was reffering to the interpretation differences of using the lh-rh diff maps or the LI maps.Bests,Gabriel.El 02/04/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:I don't know what you mean by real. Is the LI not real? The LI will remove the effect of scaling (eg, brain size).On 04/02/2013 04:48 PM, Gabriel Gonzalez Escamilla wrote: So, this means that the real differences is as Yizhou wrote? One measures the asymmetry (measured as the difference between lh-rh), and the LI or --paired-diff-norm will tell the extent of this asymmetry. Regards, Gabriel. El 02/04/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: sorry, I misspoke, the p-value will be different (perhaps very different) between LI and --paired-diff. The p-value should not change between LI and --paired-diff-norm; these two maps differ only by a scale which is removed in the t-ratio. doug On 04/02/2013 01:15 PM, Yizhou Ma wrote: If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff dougIn my opinion, the interpretation will be different, and the difference just depends on the difference between (lh-rh) and LI themselves. The former tells you if the lh is bigger than the rh in absolute values, while the latter tells you to what extent it is asymmetrical. The latter is not a scaled, but a standarized version of the former. Which you use in your study really depends on which you are interested in conceptually.On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu wrote: I think it is best to do it before the smoothing, though my results did not really change when I did it after. doug On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: sorry I meant to do the division, to standarize the LI after the smoothing. El 02/04/13, *Gabriel Gonzalez Escamilla * ggon...@upo.es mailto:ggon...@upo.es ggon...@upo.es ggon...@upo.es escribió: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. Further, this division should be done before the smoothing, right? If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It
Re: [Freesurfer] mris_preproc with --xhemi
Dear Doug,Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it?standardLI = (lh-rh)/(lh+rh)FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one.Further, this division should be done before the smoothing, right?If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps?Regards,Gabriel.El 29/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ...If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etcIf you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc.Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2.Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then runmri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mghIn my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet.dougOn 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] mris_preproc with --xhemi
sorry I meant to do the division, to standarize the LI after the smoothing.El 02/04/13, Gabriel Gonzalez Escamilla ggon...@upo.es escribió:Dear Doug,Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it?standardLI = (lh-rh)/(lh+rh)FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one.Further, this division should be done before the smoothing, right?If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps?Regards,Gabriel.El 29/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ...If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etcIf you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc.Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2.Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then runmri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mghIn my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet.dougOn 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] mris_preproc with --xhemi
On 04/02/2013 12:02 PM, Gabriel Gonzalez Escamilla wrote: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. oops, sorry, you're right Further, this division should be done before the smoothing, right? I don't think it will matter. If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff doug Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ 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 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- 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 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] mris_preproc with --xhemi
I think it is best to do it before the smoothing, though my results did not really change when I did it after. doug On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: sorry I meant to do the division, to standarize the LI after the smoothing. El 02/04/13, *Gabriel Gonzalez Escamilla * ggon...@upo.es escribió: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. Further, this division should be done before the smoothing, right? If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ 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 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- 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 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] mris_preproc with --xhemi
If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff doug In my opinion, the interpretation will be different, and the difference just depends on the difference between (lh-rh) and LI themselves. The former tells you if the lh is bigger than the rh in absolute values, while the latter tells you to what extent it is asymmetrical. The latter is not a scaled, but a standarized version of the former. Which you use in your study really depends on which you are interested in conceptually. On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: I think it is best to do it before the smoothing, though my results did not really change when I did it after. doug On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: sorry I meant to do the division, to standarize the LI after the smoothing. El 02/04/13, *Gabriel Gonzalez Escamilla * ggon...@upo.es escribió: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. Further, this division should be done before the smoothing, right? If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ 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 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1
Re: [Freesurfer] mris_preproc with --xhemi
sorry, I misspoke, the p-value will be different (perhaps very different) between LI and --paired-diff. The p-value should not change between LI and --paired-diff-norm; these two maps differ only by a scale which is removed in the t-ratio. doug On 04/02/2013 01:15 PM, Yizhou Ma wrote: If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff doug In my opinion, the interpretation will be different, and the difference just depends on the difference between (lh-rh) and LI themselves. The former tells you if the lh is bigger than the rh in absolute values, while the latter tells you to what extent it is asymmetrical. The latter is not a scaled, but a standarized version of the former. Which you use in your study really depends on which you are interested in conceptually. On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I think it is best to do it before the smoothing, though my results did not really change when I did it after. doug On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: sorry I meant to do the division, to standarize the LI after the smoothing. El 02/04/13, *Gabriel Gonzalez Escamilla * ggon...@upo.es mailto:ggon...@upo.es escribió: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. Further, this division should be done before the smoothing, right? If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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
Re: [Freesurfer] mris_preproc with --xhemi
So, this means that the real differences is as Yizhou wrote?One measures the asymmetry (measured as the difference between lh-rh), and the LI or --paired-diff-norm will tell the extent of this asymmetry.Regards,Gabriel.El 02/04/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:sorry, I misspoke, the p-value will be different (perhaps very different) between LI and --paired-diff. The p-value should not change between LI and --paired-diff-norm; these two maps differ only by a scale which is removed in the t-ratio.dougOn 04/02/2013 01:15 PM, Yizhou Ma wrote: If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff doug In my opinion, the interpretation will be different, and the difference just depends on the difference between (lh-rh) and LI themselves. The former tells you if the lh is bigger than the rh in absolute values, while the latter tells you to what extent it is asymmetrical. The latter is not a scaled, but a standarized version of the former. Which you use in your study really depends on which you are interested in conceptually. On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu wrote: I think it is best to do it before the smoothing, though my results did not really change when I did it after. doug On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: sorry I meant to do the division, to standarize the LI after the smoothing. El 02/04/13, *Gabriel Gonzalez Escamilla * ggon...@upo.es mailto:ggon...@upo.es ggon...@upo.es escribió: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. Further, this division should be done before the smoothing, right? If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.
Re: [Freesurfer] mris_preproc with --xhemi
I don't know what you mean by real. Is the LI not real? The LI will remove the effect of scaling (eg, brain size). On 04/02/2013 04:48 PM, Gabriel Gonzalez Escamilla wrote: So, this means that the real differences is as Yizhou wrote? One measures the asymmetry (measured as the difference between lh-rh), and the LI or --paired-diff-norm will tell the extent of this asymmetry. Regards, Gabriel. El 02/04/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: sorry, I misspoke, the p-value will be different (perhaps very different) between LI and --paired-diff. The p-value should not change between LI and --paired-diff-norm; these two maps differ only by a scale which is removed in the t-ratio. doug On 04/02/2013 01:15 PM, Yizhou Ma wrote: If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff doug In my opinion, the interpretation will be different, and the difference just depends on the difference between (lh-rh) and LI themselves. The former tells you if the lh is bigger than the rh in absolute values, while the latter tells you to what extent it is asymmetrical. The latter is not a scaled, but a standarized version of the former. Which you use in your study really depends on which you are interested in conceptually. On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu wrote: I think it is best to do it before the smoothing, though my results did not really change when I did it after. doug On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: sorry I meant to do the division, to standarize the LI after the smoothing. El 02/04/13, *Gabriel Gonzalez Escamilla * ggon...@upo.es mailto:ggon...@upo.es ggon...@upo.es escribió: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. Further, this division should be done before the smoothing, right? If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the
[Freesurfer] mris_preproc with --xhemi
Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ 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] mris_preproc with --xhemi
The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ 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 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.
Re: [Freesurfer] mris_preproc with --xhemi
Thanks, Doug. This is very helpful! On Fri, Mar 29, 2013 at 12:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ 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 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 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.
