Hi! I am trying to do a conjunction analysis using mri_concat --conjunct with 2 to three sig.nii as input. It seems to me that the resulting map is what Nichols et al. refer to as MS/GN, i.e., a test against the global null (at least one effect). Is that correct, and does that depends on v4.5 / 5.x? Is there something in FSFAST that would allow me to do a "real" conjunction, that is, all effects significant in a given voxel? Thanks, Caspar
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about your fsfast question. There is nothing to automatically do it (ie, you'll need to run mri_concat) doug On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
Hi! I am trying to do a conjunction analysis using mri_concat --conjunct with 2 to three sig.nii as input. It seems to me that the resulting map is what Nichols et al. refer to as MS/GN, i.e., a test against the global null (at least one effect). Is that correct, and does that depends on v4.5 / 5.x? Is there something in FSFAST that would allow me to do a "real" conjunction, that is, all effects significant in a given voxel? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, I am trying to implement something like the MS/CN conjunction suggested by Nichols. For that, I am finding the voxels that show a significant effect at a given threshold in both contrast maps. I have one question about the resulting p-value. In principle, I would tend to think that the conjunction p-value is p-value of contrast1 x p-value of contrast 2, e.g., 0.05*0.05=0.0025. However, one could also think that it is the max of the two p-values. Which one is correct? Thanks, Caspar
2013/5/23 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about your fsfast question. There is nothing to automatically do it (ie, you'll need to run mri_concat) doug On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
Hi! I am trying to do a conjunction analysis using mri_concat --conjunct with 2 to three sig.nii as input. It seems to me that the resulting map is what Nichols et al. refer to as MS/GN, i.e., a test against the global null (at least one effect). Is that correct, and does that depends on v4.5 / 5.x? Is there something in FSFAST that would allow me to do a "real" conjunction, that is, all effects significant in a given voxel? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
The way to do it is to take the maximum p-value at each voxel (this is what mri_concat does). doug
On 05/24/2013 02:10 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, I am trying to implement something like the MS/CN conjunction suggested by Nichols. For that, I am finding the voxels that show a significant effect at a given threshold in both contrast maps. I have one question about the resulting p-value. In principle, I would tend to think that the conjunction p-value is p-value of contrast1 x p-value of contrast 2, e.g., 0.05*0.05=0.0025. However, one could also think that it is the max of the two p-values. Which one is correct? Thanks, Caspar
2013/5/23 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about your fsfast question. There is nothing to automatically do it (ie, you'll need to run mri_concat) doug On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
Hi! I am trying to do a conjunction analysis using mri_concat --conjunct with 2 to three sig.nii as input. It seems to me that the resulting map is what Nichols et al. refer to as MS/GN, i.e., a test against the global null (at least one effect). Is that correct, and does that depends on v4.5 / 5.x? Is there something in FSFAST that would allow me to do a "real" conjunction, that is, all effects significant in a given voxel? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Doug, just to make sure I understand you right: No matter whether I want to test a conjunction a la Friston (any voxel significant, this is what mri_concat gives) or a la Nichols (both voxels significant), I would take the maximum p-value, correct? What about multiple comparisons? Would you threshold the two contrast maps individually, /and or the resulting comjunction map? And if I would like to use cluster size thresholding, how would I get the smoothness estimate for the conjunction map? Thanks, Caspar
2013/5/24 Douglas N Greve greve@nmr.mgh.harvard.edu:
The way to do it is to take the maximum p-value at each voxel (this is what mri_concat does). doug
On 05/24/2013 02:10 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, I am trying to implement something like the MS/CN conjunction suggested by Nichols. For that, I am finding the voxels that show a significant effect at a given threshold in both contrast maps. I have one question about the resulting p-value. In principle, I would tend to think that the conjunction p-value is p-value of contrast1 x p-value of contrast 2, e.g., 0.05*0.05=0.0025. However, one could also think that it is the max of the two p-values. Which one is correct? Thanks, Caspar
2013/5/23 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about your fsfast question. There is nothing to automatically do it (ie, you'll need to run mri_concat) doug On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
Hi! I am trying to do a conjunction analysis using mri_concat --conjunct with 2 to three sig.nii as input. It seems to me that the resulting map is what Nichols et al. refer to as MS/GN, i.e., a test against the global null (at least one effect). Is that correct, and does that depends on v4.5 / 5.x? Is there something in FSFAST that would allow me to do a "real" conjunction, that is, all effects significant in a given voxel? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
oops, sorry, mri_concat takes the smallest p-value (and so implements Nichols). I think I'd to the multiple comparisons correction after conjunction (but I'd like to hear opinions). Not sure about the FWHM, probably take the max of the contrasts that go into it.
doug
On 05/24/2013 03:02 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, just to make sure I understand you right: No matter whether I want to test a conjunction a la Friston (any voxel significant, this is what mri_concat gives) or a la Nichols (both voxels significant), I would take the maximum p-value, correct? What about multiple comparisons? Would you threshold the two contrast maps individually, /and or the resulting comjunction map? And if I would like to use cluster size thresholding, how would I get the smoothness estimate for the conjunction map? Thanks, Caspar
2013/5/24 Douglas N Greve greve@nmr.mgh.harvard.edu:
The way to do it is to take the maximum p-value at each voxel (this is what mri_concat does). doug
On 05/24/2013 02:10 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, I am trying to implement something like the MS/CN conjunction suggested by Nichols. For that, I am finding the voxels that show a significant effect at a given threshold in both contrast maps. I have one question about the resulting p-value. In principle, I would tend to think that the conjunction p-value is p-value of contrast1 x p-value of contrast 2, e.g., 0.05*0.05=0.0025. However, one could also think that it is the max of the two p-values. Which one is correct? Thanks, Caspar
2013/5/23 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about your fsfast question. There is nothing to automatically do it (ie, you'll need to run mri_concat) doug On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
Hi! I am trying to do a conjunction analysis using mri_concat --conjunct with 2 to three sig.nii as input. It seems to me that the resulting map is what Nichols et al. refer to as MS/GN, i.e., a test against the global null (at least one effect). Is that correct, and does that depends on v4.5 / 5.x? Is there something in FSFAST that would allow me to do a "real" conjunction, that is, all effects significant in a given voxel? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi Doug, I also have a tendency towards correcting the conjunction map. Regarding mri_concat: If I understand the results correctly, it does not exactly implement Nichols. It seems to give voxels even if they are only significant in one contrast, which is exactly what Nichols et al argued against. In the Nichols sense, you have to threshold the two contrast maps and a voxel will only be considered significant for the conjunction if there is a logical AND, i.e., both contrasts are significant at that threshold. Caspar
2013/5/24 Douglas N Greve greve@nmr.mgh.harvard.edu:
oops, sorry, mri_concat takes the smallest p-value (and so implements Nichols). I think I'd to the multiple comparisons correction after conjunction (but I'd like to hear opinions). Not sure about the FWHM, probably take the max of the contrasts that go into it.
doug
On 05/24/2013 03:02 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, just to make sure I understand you right: No matter whether I want to test a conjunction a la Friston (any voxel significant, this is what mri_concat gives) or a la Nichols (both voxels significant), I would take the maximum p-value, correct? What about multiple comparisons? Would you threshold the two contrast maps individually, /and or the resulting comjunction map? And if I would like to use cluster size thresholding, how would I get the smoothness estimate for the conjunction map? Thanks, Caspar
2013/5/24 Douglas N Greve greve@nmr.mgh.harvard.edu:
The way to do it is to take the maximum p-value at each voxel (this is what mri_concat does). doug
On 05/24/2013 02:10 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, I am trying to implement something like the MS/CN conjunction suggested by Nichols. For that, I am finding the voxels that show a significant effect at a given threshold in both contrast maps. I have one question about the resulting p-value. In principle, I would tend to think that the conjunction p-value is p-value of contrast1 x p-value of contrast 2, e.g., 0.05*0.05=0.0025. However, one could also think that it is the max of the two p-values. Which one is correct? Thanks, Caspar
2013/5/23 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about your fsfast question. There is nothing to automatically do it (ie, you'll need to run mri_concat) doug On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
Hi! I am trying to do a conjunction analysis using mri_concat --conjunct with 2 to three sig.nii as input. It seems to me that the resulting map is what Nichols et al. refer to as MS/GN, i.e., a test against the global null (at least one effect). Is that correct, and does that depends on v4.5 / 5.x? Is there something in FSFAST that would allow me to do a "real" conjunction, that is, all effects significant in a given voxel? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
oops, sorry again.It will give the maximum p-value, not the min. This implements Nichols. If you threshold the map at a given level, it will show you what you would have gotten had you applied that threshold to both mapsand then computed an AND. Doing this way means that you can choose your threshold after you do the conjunction. doug
On 05/24/2013 03:10 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, I also have a tendency towards correcting the conjunction map. Regarding mri_concat: If I understand the results correctly, it does not exactly implement Nichols. It seems to give voxels even if they are only significant in one contrast, which is exactly what Nichols et al argued against. In the Nichols sense, you have to threshold the two contrast maps and a voxel will only be considered significant for the conjunction if there is a logical AND, i.e., both contrasts are significant at that threshold. Caspar
2013/5/24 Douglas N Greve greve@nmr.mgh.harvard.edu:
oops, sorry, mri_concat takes the smallest p-value (and so implements Nichols). I think I'd to the multiple comparisons correction after conjunction (but I'd like to hear opinions). Not sure about the FWHM, probably take the max of the contrasts that go into it.
doug
On 05/24/2013 03:02 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, just to make sure I understand you right: No matter whether I want to test a conjunction a la Friston (any voxel significant, this is what mri_concat gives) or a la Nichols (both voxels significant), I would take the maximum p-value, correct? What about multiple comparisons? Would you threshold the two contrast maps individually, /and or the resulting comjunction map? And if I would like to use cluster size thresholding, how would I get the smoothness estimate for the conjunction map? Thanks, Caspar
2013/5/24 Douglas N Greve greve@nmr.mgh.harvard.edu:
The way to do it is to take the maximum p-value at each voxel (this is what mri_concat does). doug
On 05/24/2013 02:10 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, I am trying to implement something like the MS/CN conjunction suggested by Nichols. For that, I am finding the voxels that show a significant effect at a given threshold in both contrast maps. I have one question about the resulting p-value. In principle, I would tend to think that the conjunction p-value is p-value of contrast1 x p-value of contrast 2, e.g., 0.05*0.05=0.0025. However, one could also think that it is the max of the two p-values. Which one is correct? Thanks, Caspar
2013/5/23 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about your fsfast question. There is nothing to automatically do it (ie, you'll need to run mri_concat) doug On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote: > Hi! > I am trying to do a conjunction analysis using mri_concat --conjunct > with 2 to three sig.nii as input. > It seems to me that the resulting map is what Nichols et al. refer to > as MS/GN, i.e., a test against the global null (at least one effect). > Is that correct, and does that depends on v4.5 / 5.x? > Is there something in FSFAST that would allow me to do a "real" > conjunction, that is, all effects significant in a given voxel? > Thanks, Caspar > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
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Caspar M. Schwiedrzik -
Douglas N Greve