External Email - Use Caution
Dear Freesurfer experts,
I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
I have followed the group analysis tutorial ( https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA... ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces
However, I have two questions regarding this issue:
1) I would like to know whether is it correct to use for example --cache 3 or 2 instead of 4. Is it recommended?
2) Is it better to use, instead of the above Z Monte Carlo simulation command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1
Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one.
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
External Email - Use Caution
Dear Freesurfer experts,
I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#GLMAnalys... https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29 ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdirlh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue:
- I would like to know whether is it correct to use for example
--cache 3 or 2 instead of 4. Is it recommended?
Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.
- Is it better to use, instead of the above Z Monte Carlo simulation
command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1
The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.
Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one.
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Douglas,
I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses? Thank you very much.
Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Freesurfer experts,
I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/126m93QA85w-J22Vo42Au1lb9NHKfXfjy9vO-I9N9Tb9C8_... https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29 ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue:
- I would like to know whether is it correct to use for example --cache 3
or 2 instead of 4. Is it recommended?
Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.
- Is it better to use, instead of the above Z Monte Carlo simulation
command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1
The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.
Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one.
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRS...
That is ok for thickness, but not for volume
On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
External Email - Use Caution
Dear Douglas,
I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses? Thank you very much.
Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (<dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>) escribió:
On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:External Email - Use Caution Dear Freesurfer experts, I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#GLMAnalysis.28mriglmfit.29 <https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29> ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdirlh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue: 1) I would like to know whether is it correct to use for example --cache 3 or 2 instead of 4. Is it recommended?Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.2) Is it better to use, instead of the above Z Monte Carlo simulation command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one. Thank you very much in advance. Kind regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es <http://secure-web.cisco.com/1UnrLWQpMMxdhKEG5HMrtIxWFxHsJTfrtXypEo9Dc-98NFX_4yPEsg2NqEqoQuReypFHAGq0aXxq1CsKiplAUMhJn3xTUmF95qk9IYP-L7373YTN8T8-RJR55wA1Gnu3iuM4MUGQwMR6SqTrWHWlhNVRjSS5BnRoz0lysXBO8ghrHRFlB-03jBzASp5QQha90nwuyk6z1jyP2lupIfhaAxZToPr7Ae2fnuSSJSl8bWpvgdWV6goduAv0Kk67utWKpRwjrBlEZcLB8IsAawzINIA/http%3A%2F%2Fneurolab.deusto.es%2F> Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Dear Douglas,
So, as far as I understand you, if I use a smoothing of 15 I can use a --cache of 2 in thickness analysis, but I should use a higher --cache for volume, such as 3. Is that correct? And would you recommend me using another smoothing level?
Thank you very much for your help. Kind regards,
Agurne
El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
That is ok for thickness, but not for volume
On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses? Thank you very much.
Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Freesurfer experts,
I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1gUhAGwIcIwg0D0GDpPhB3YT_PiU6nUgQhmrC09LKHkoyNO... https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29 ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue:
- I would like to know whether is it correct to use for example --cache
3 or 2 instead of 4. Is it recommended?
Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.
- Is it better to use, instead of the above Z Monte Carlo simulation
command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1
The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.
Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one.
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1nJ4gjNQd-sMNynA7lIv2rMCcwV1jhv9TsavnMyvr1_WsqE... https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of this paper
False positive rates in surface-based anatomical analysis Douglas N. Greve a, b, * , Bruce Fischl a, b
On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:
External Email - Use Caution
Dear Douglas,
So, as far as I understand you, if I use a smoothing of 15 I can use a --cache of 2 in thickness analysis, but I should use a higher --cache for volume, such as 3. Is that correct? And would you recommend me using another smoothing level?
Thank you very much for your help. Kind regards,
Agurne
El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (<dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>) escribió:
That is ok for thickness, but not for volume On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:External Email - Use Caution Dear Douglas, I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses? Thank you very much. Best regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es <http://secure-web.cisco.com/13eL9VR1VrodsUjbGEsZKkii7H_4oFZ6JxkEjznjOHcNJSomvo7PoohKYqpfxYid2YLiqoCqS5t8lJJ8k7SGmRZW-Rrm49cqfk_FsYsh7lkHSA9hqJ4ZxCfKQvg098WrxcBQpfdHuiHniE4q0YxaN-oJGKdXw3at7j8wpNKKd1s0brILkj9hn70avIjpNZuR5rOGF4V_HoqoIoUMMn-Usc5TK09H0PoLHqXRJwtTE6xtDfrtLLG4yfDvmLs3bJM5JwAJWOMKclbenIec2VPBKjw/http%3A%2F%2Fneurolab.deusto.es%2F> Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribió: On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:External Email - Use Caution Dear Freesurfer experts, I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#GLMAnalysis.28mriglmfit.29 <https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29> ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdirlh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue: 1) I would like to know whether is it correct to use for example --cache 3 or 2 instead of 4. Is it recommended?Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.2) Is it better to use, instead of the above Z Monte Carlo simulation command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one. Thank you very much in advance. Kind regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es <http://secure-web.cisco.com/1UnrLWQpMMxdhKEG5HMrtIxWFxHsJTfrtXypEo9Dc-98NFX_4yPEsg2NqEqoQuReypFHAGq0aXxq1CsKiplAUMhJn3xTUmF95qk9IYP-L7373YTN8T8-RJR55wA1Gnu3iuM4MUGQwMR6SqTrWHWlhNVRjSS5BnRoz0lysXBO8ghrHRFlB-03jBzASp5QQha90nwuyk6z1jyP2lupIfhaAxZToPr7Ae2fnuSSJSl8bWpvgdWV6goduAv0Kk67utWKpRwjrBlEZcLB8IsAawzINIA/http%3A%2F%2Fneurolab.deusto.es%2F> Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1nJ4gjNQd-sMNynA7lIv2rMCcwV1jhv9TsavnMyvr1_WsqEkNk30tKz3VJleOt5ehMd8LapXi1FBVJHWToBOBaYDrF0UI9s0vAcvi90NXpJnj3HjO8Skl_8QEAibD8VHRXVuguTEp6LzhZVqPLWqYOgfOo1VMYhfiy7HGa2eAEcMF-0V0piC7o8jLyFMgmejyssrx1Tdk7-c2y39CBqCcjvAin-nr0oAUYwJafCVwG-6Rj5mSsA_tYMAQcSCSlqSoEuxSwqVgZdCVAEVpQ57Ldw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1nJ4gjNQd-sMNynA7lIv2rMCcwV1jhv9TsavnMyvr1_WsqEkNk30tKz3VJleOt5ehMd8LapXi1FBVJHWToBOBaYDrF0UI9s0vAcvi90NXpJnj3HjO8Skl_8QEAibD8VHRXVuguTEp6LzhZVqPLWqYOgfOo1VMYhfiy7HGa2eAEcMF-0V0piC7o8jLyFMgmejyssrx1Tdk7-c2y39CBqCcjvAin-nr0oAUYwJafCVwG-6Rj5mSsA_tYMAQcSCSlqSoEuxSwqVgZdCVAEVpQ57Ldw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Dear Douglas, Thank you very much ! This paper is very helpful. Regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 17:55, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of this paper
False positive rates in surface-based anatomical analysis Douglas N. Greve a, b, * , Bruce Fischl a, b
On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
So, as far as I understand you, if I use a smoothing of 15 I can use a --cache of 2 in thickness analysis, but I should use a higher --cache for volume, such as 3. Is that correct? And would you recommend me using another smoothing level?
Thank you very much for your help. Kind regards,
Agurne
El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
That is ok for thickness, but not for volume
On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses? Thank you very much.
Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Freesurfer experts,
I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1YYXPkjCyzOxcthjmbe9eEO8POSyi-gHOxWGS_5KIwRmlx8... https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29 ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue:
- I would like to know whether is it correct to use for example --cache
3 or 2 instead of 4. Is it recommended?
Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.
- Is it better to use, instead of the above Z Monte Carlo simulation
command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1
The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.
Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one.
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1SiFvBHyyzZkM_vhp66Q4k3B7AJC1YQOiJ5rtypxmX1Jc2v... https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Dear Douglas,
I have another question regarding multiple comparisons correction:
Can I use --cache with volume analyses? Or should I use --grf?
Thank you very much,
Kind regards,
Agurne
El mar, 9 feb 2021 a las 18:11, Agurne Sampedro Calvete (< a.sampedro@deusto.es>) escribió:
Dear Douglas, Thank you very much ! This paper is very helpful. Regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 17:55, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of this paper
False positive rates in surface-based anatomical analysis Douglas N. Greve a, b, * , Bruce Fischl a, b
On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
So, as far as I understand you, if I use a smoothing of 15 I can use a --cache of 2 in thickness analysis, but I should use a higher --cache for volume, such as 3. Is that correct? And would you recommend me using another smoothing level?
Thank you very much for your help. Kind regards,
Agurne
El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
That is ok for thickness, but not for volume
On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses? Thank you very much.
Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (< dgreve@mgh.harvard.edu>) escribió:
On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Freesurfer experts,
I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1_wpkFmQ6nZFQp0yOHorX-pT7wGKx8HuLLx3_ANldnkgimr... https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29 ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue:
- I would like to know whether is it correct to use for example
--cache 3 or 2 instead of 4. Is it recommended?
Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.
- Is it better to use, instead of the above Z Monte Carlo simulation
command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1
The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.
Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one.
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
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You have to use --grf. I never computed the cache tables for volumes
On 2/19/2021 9:58 AM, Agurne Sampedro Calvete wrote:
External Email - Use Caution
Dear Douglas,
I have another question regarding multiple comparisons correction:
Can I use --cache with volume analyses? Or should I use --grf?
Thank you very much,
Kind regards,
Agurne
El mar, 9 feb 2021 a las 18:11, Agurne Sampedro Calvete (<a.sampedro@deusto.es mailto:a.sampedro@deusto.es>) escribió:
Dear Douglas, Thank you very much ! This paper is very helpful. Regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es <http://secure-web.cisco.com/1gAJEBCib9EW_ylULEVTDxDzASq_VMOoRAEIWgk_u4ErJ721bCC2wiEnNjrODzdkLXlIUmUsYnhRRjqDLlF1-Bcqys-mlDb_B2aTcm6ye1Dz08XxAm-e9QCfnFqpX3YHhkIc2TwFKsIgxRQHJTeEGrtW6m1ChKXBspuFtzKRQDbCSxIQwo8tPHgJQdt9teXZw8JgsVDegLEiWNU5Irfgx1a21XBWZK-Milh5gONHp111_8KEVyVoe2qdUfPqrPAclArlqk37HtX-_zSCMbxRkHQ/http%3A%2F%2Fneurolab.deusto.es%2F> Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) El mar, 9 feb 2021 a las 17:55, Douglas N. Greve (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribió: Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of this paper False positive rates in surface-based anatomical analysis Douglas N. Greve a, b, * , Bruce Fischl a, b On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:External Email - Use Caution Dear Douglas, So, as far as I understand you, if I use a smoothing of 15 I can use a --cache of 2 in thickness analysis, but I should use a higher --cache for volume, such as 3. Is that correct? And would you recommend me using another smoothing level? Thank you very much for your help. Kind regards, Agurne El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribió: That is ok for thickness, but not for volume On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:External Email - Use Caution Dear Douglas, I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses? Thank you very much. Best regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es <http://secure-web.cisco.com/13eL9VR1VrodsUjbGEsZKkii7H_4oFZ6JxkEjznjOHcNJSomvo7PoohKYqpfxYid2YLiqoCqS5t8lJJ8k7SGmRZW-Rrm49cqfk_FsYsh7lkHSA9hqJ4ZxCfKQvg098WrxcBQpfdHuiHniE4q0YxaN-oJGKdXw3at7j8wpNKKd1s0brILkj9hn70avIjpNZuR5rOGF4V_HoqoIoUMMn-Usc5TK09H0PoLHqXRJwtTE6xtDfrtLLG4yfDvmLs3bJM5JwAJWOMKclbenIec2VPBKjw/http%3A%2F%2Fneurolab.deusto.es%2F> Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribió: On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:External Email - Use Caution Dear Freesurfer experts, I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#GLMAnalysis.28mriglmfit.29 <https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29> ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdirlh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue: 1) I would like to know whether is it correct to use for example --cache 3 or 2 instead of 4. Is it recommended?Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.2) Is it better to use, instead of the above Z Monte Carlo simulation command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one. Thank you very much in advance. Kind regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es <http://secure-web.cisco.com/1UnrLWQpMMxdhKEG5HMrtIxWFxHsJTfrtXypEo9Dc-98NFX_4yPEsg2NqEqoQuReypFHAGq0aXxq1CsKiplAUMhJn3xTUmF95qk9IYP-L7373YTN8T8-RJR55wA1Gnu3iuM4MUGQwMR6SqTrWHWlhNVRjSS5BnRoz0lysXBO8ghrHRFlB-03jBzASp5QQha90nwuyk6z1jyP2lupIfhaAxZToPr7Ae2fnuSSJSl8bWpvgdWV6goduAv0Kk67utWKpRwjrBlEZcLB8IsAawzINIA/http%3A%2F%2Fneurolab.deusto.es%2F> Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1nJ4gjNQd-sMNynA7lIv2rMCcwV1jhv9TsavnMyvr1_WsqEkNk30tKz3VJleOt5ehMd8LapXi1FBVJHWToBOBaYDrF0UI9s0vAcvi90NXpJnj3HjO8Skl_8QEAibD8VHRXVuguTEp6LzhZVqPLWqYOgfOo1VMYhfiy7HGa2eAEcMF-0V0piC7o8jLyFMgmejyssrx1Tdk7-c2y39CBqCcjvAin-nr0oAUYwJafCVwG-6Rj5mSsA_tYMAQcSCSlqSoEuxSwqVgZdCVAEVpQ57Ldw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1nJ4gjNQd-sMNynA7lIv2rMCcwV1jhv9TsavnMyvr1_WsqEkNk30tKz3VJleOt5ehMd8LapXi1FBVJHWToBOBaYDrF0UI9s0vAcvi90NXpJnj3HjO8Skl_8QEAibD8VHRXVuguTEp6LzhZVqPLWqYOgfOo1VMYhfiy7HGa2eAEcMF-0V0piC7o8jLyFMgmejyssrx1Tdk7-c2y39CBqCcjvAin-nr0oAUYwJafCVwG-6Rj5mSsA_tYMAQcSCSlqSoEuxSwqVgZdCVAEVpQ57Ldw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1_eqzx9LmMcJt42ZWiXWynEDaQ6WqZ_ON1qgZBuXepyP20D1dzerubsAj2bkoprPCSkh1X5Pgc2fJ_i7OxXDRpdvomcJ0_6Yn9vuyBi6NGoYbXL-Cj7lVz_CegHtbtDf1xzMIOVt7mO83D7g9AGgoYKjCWgdu7Y78i3qNV8-1NpGeELLQ9YJSwr_pN_etQGsrnIBzFql9F8WUw1bOBy39AMhNBGRXhrjtQoKKHkNTDUCdw5zoou3E2HywUYvc-s8Lu-fetlHRcTj0smthjROCrQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1_eqzx9LmMcJt42ZWiXWynEDaQ6WqZ_ON1qgZBuXepyP20D1dzerubsAj2bkoprPCSkh1X5Pgc2fJ_i7OxXDRpdvomcJ0_6Yn9vuyBi6NGoYbXL-Cj7lVz_CegHtbtDf1xzMIOVt7mO83D7g9AGgoYKjCWgdu7Y78i3qNV8-1NpGeELLQ9YJSwr_pN_etQGsrnIBzFql9F8WUw1bOBy39AMhNBGRXhrjtQoKKHkNTDUCdw5zoou3E2HywUYvc-s8Lu-fetlHRcTj0smthjROCrQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Dear Douglas,
And can I include abs to the --grf 3 command? I read this in the tutorial: "NOTE: the "abs" for GRF is only approximate. For volumes, it may give very conservative results" Is it better to include neg or pos? Thank you! Regards,
Agurne
El vie, 19 feb 2021 a las 16:29, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
You have to use --grf. I never computed the cache tables for volumes
On 2/19/2021 9:58 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
I have another question regarding multiple comparisons correction:
Can I use --cache with volume analyses? Or should I use --grf?
Thank you very much,
Kind regards,
Agurne
El mar, 9 feb 2021 a las 18:11, Agurne Sampedro Calvete (< a.sampedro@deusto.es>) escribió:
Dear Douglas, Thank you very much ! This paper is very helpful. Regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 17:55, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of this paper
False positive rates in surface-based anatomical analysis Douglas N. Greve a, b, * , Bruce Fischl a, b
On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
So, as far as I understand you, if I use a smoothing of 15 I can use a --cache of 2 in thickness analysis, but I should use a higher --cache for volume, such as 3. Is that correct? And would you recommend me using another smoothing level?
Thank you very much for your help. Kind regards,
Agurne
El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (< dgreve@mgh.harvard.edu>) escribió:
That is ok for thickness, but not for volume
On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses? Thank you very much.
Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (< dgreve@mgh.harvard.edu>) escribió:
On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Freesurfer experts,
I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1uvView0TBMBZs9iGxZOYS5oZs4yszqMCsJpC17YEyDqbVz... https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29 ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue:
- I would like to know whether is it correct to use for example
--cache 3 or 2 instead of 4. Is it recommended?
Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.
- Is it better to use, instead of the above Z Monte Carlo simulation
command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1
The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.
Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one.
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8D... https://secure-web.cisco.com/1nJ4gjNQd-sMNynA7lIv2rMCcwV1jhv9TsavnMyvr1_WsqEkNk30tKz3VJleOt5ehMd8LapXi1FBVJHWToBOBaYDrF0UI9s0vAcvi90NXpJnj3HjO8Skl_8QEAibD8VHRXVuguTEp6LzhZVqPLWqYOgfOo1VMYhfiy7HGa2eAEcMF-0V0piC7o8jLyFMgmejyssrx1Tdk7-c2y39CBqCcjvAin-nr0oAUYwJafCVwG-6Rj5mSsA_tYMAQcSCSlqSoEuxSwqVgZdCVAEVpQ57Ldw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8D... https://secure-web.cisco.com/1nJ4gjNQd-sMNynA7lIv2rMCcwV1jhv9TsavnMyvr1_WsqEkNk30tKz3VJleOt5ehMd8LapXi1FBVJHWToBOBaYDrF0UI9s0vAcvi90NXpJnj3HjO8Skl_8QEAibD8VHRXVuguTEp6LzhZVqPLWqYOgfOo1VMYhfiy7HGa2eAEcMF-0V0piC7o8jLyFMgmejyssrx1Tdk7-c2y39CBqCcjvAin-nr0oAUYwJafCVwG-6Rj5mSsA_tYMAQcSCSlqSoEuxSwqVgZdCVAEVpQ57Ldw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8D... https://secure-web.cisco.com/1_eqzx9LmMcJt42ZWiXWynEDaQ6WqZ_ON1qgZBuXepyP20D1dzerubsAj2bkoprPCSkh1X5Pgc2fJ_i7OxXDRpdvomcJ0_6Yn9vuyBi6NGoYbXL-Cj7lVz_CegHtbtDf1xzMIOVt7mO83D7g9AGgoYKjCWgdu7Y78i3qNV8-1NpGeELLQ9YJSwr_pN_etQGsrnIBzFql9F8WUw1bOBy39AMhNBGRXhrjtQoKKHkNTDUCdw5zoou3E2HywUYvc-s8Lu-fetlHRcTj0smthjROCrQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8D... https://secure-web.cisco.com/1_eqzx9LmMcJt42ZWiXWynEDaQ6WqZ_ON1qgZBuXepyP20D1dzerubsAj2bkoprPCSkh1X5Pgc2fJ_i7OxXDRpdvomcJ0_6Yn9vuyBi6NGoYbXL-Cj7lVz_CegHtbtDf1xzMIOVt7mO83D7g9AGgoYKjCWgdu7Y78i3qNV8-1NpGeELLQ9YJSwr_pN_etQGsrnIBzFql9F8WUw1bOBy39AMhNBGRXhrjtQoKKHkNTDUCdw5zoou3E2HywUYvc-s8Lu-fetlHRcTj0smthjROCrQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/100wbztRmR4HEvnZpXHB_F_6Y7g1QUGQiPJDgI2b9Az2n8D...
freesurfer@nmr.mgh.harvard.edu
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Agurne Sampedro Calvete -
Douglas N. Greve