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Dear FreeSurfer Developers,
we have a longitudinal study design with one group and ran a paired analysis in FreeSurfer V6 (as described here: https://secure-web.cisco.com/1V0gSNyIvhCtX3j8K-mzIp_bu0OnK1ZDZxKlOeenlA2T-l0...). Afterwards we corrected for multiple comparisons (as described here: https://secure-web.cisco.com/1kF3xxriMcabTqMwlV5PjrV7Bz3-ihiWEkX08AlNLpslyHg...).
One cluster showed a significant change for cortical thickness and the average values of each subject were located in the “y.ocn.dat”.
However, we are now wondering how it is possible to get the individual pre- and post-values for that specific cluster for all subjects. Is there any method to do so?
Any assistance is very much appreciated!
Thanks in advance.
Best,
Franziska
Dr. Franziska Mund
Wissenschaftliche Mitarbeiterin
Sportmedizinisches Institut
Warburger Straße 100
33098 Paderborn
Raum SP.0.508
Telefon +49 5251 60-3187
Mail mund@sportmed.uni-paderborn.demailto:mund@sportmed.uni-paderborn.de
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Yes, you can run something like mri_segstats --i stack1.mgz --seg ocn.mgz --avgwf subject.vals1.dat --excludeid 0 --sum sum1.dat where stack1.mgz is the stack of subjects in fsaverage space from time point 1 The output subject.val1.dat will have a row for each subject and a column for each cluster. The value will be the average value from that subject over the voxels in that cluster
On 7/31/2025 9:26 AM, Franziska Mund wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
we have a longitudinal study design with one group and ran a paired analysis in FreeSurfer V6 (as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis https://secure-web.cisco.com/1V0gSNyIvhCtX3j8K-mzIp_bu0OnK1ZDZxKlOeenlA2T-l0CCdlEjkvqSe_5KXnd2BsF6h2tMQlWydqH1m8dKAmoCEpn-TbkFaHJWOqGpSYtRU8YvMgQzcP2QDPVw3azcRBFW9C1XlQKk7m8bMYYozP3nmdcvhYw0JYyhHjkoxQOgcnd0zYH4S7XaSVtvWRFD4r_MjbvM8iG-0t0lmqJbYtixgRh3XHMAtobqfTEdgrqNk_fjPSL2M5iEDFemk9Hrlavuirl3qGaFh1WcfeX9q_SI8y8ZY4bIoYk8BnOINqrgvbl8EIJ2YvLhfqSqnz1c6lWT0TuWLUcnXChPRCK_YQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis). Afterwards we corrected for multiple comparisons (as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0 https://secure-web.cisco.com/1kF3xxriMcabTqMwlV5PjrV7Bz3-ihiWEkX08AlNLpslyHgUOXeF8fr5ulAvLPcyf8uMHq8hloj1Y0krgnu9ohcGi3EnBNppfRwRcB9TLq05apD-eGE0K0CzTmSAcVmw2etFiVP5PgwWAwPHUk7JIZrQVUVLi2EUia9T1UWuxO0p9FoioElKpdbAyBIeUJ7NH1O8Ihf4t4SWLnIDfP9Q5N_iL13R5ypa0TFVO14wZu8IhSGemg9TvCJHE2p5ES8a9ByJ1j715uelFLXsf_fr8VmOnWc-UAAujQ7EcU9n-yoDUBI_EAwXM5TAJJX57AVmv5Kmp850i96_x9yuV1H5kxw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0).
One cluster showed a significant change for cortical thickness and the average values of each subject were located in the “y.ocn.dat”.
However, we are now wondering how it is possible to get the individual pre- and post-values for that specific cluster for all subjects. Is there any method to do so?
Any assistance is very much appreciated!
Thanks in advance.
Best,
Franziska
*Dr. Franziska Mund *
Wissenschaftliche Mitarbeiterin
Sportmedizinisches Institut
Warburger Straße 100
33098 Paderborn
*Raum*SP.0.508
*Telefon*+49 5251 60-3187
*Mail*mund@sportmed.uni-paderborn.de mailto:mund@sportmed.uni-paderborn.de
UPB Instagram https://secure-web.cisco.com/1Nd--jQ71ePt5LJ_Wmk5O8d4Kr2kWpH55lAu0v9n9LQVjGkAK2OvaY-0hzOTmur1S1r97wZpiljAeAP9X4E4ca9yMCH-RLdBDF1I3v6XeHvzcRMZdciDTjk2znIoB8HQ4xbTcspDu-74JwC7fWIJ3ehtriVAJ8Y6aEY5EAk6I4b9rV0zIxiCfjatioE7kYsRZy35DaAllb2kTQiZ94jPmLpx5D2LPZ44UTWLdqWUJd4jyf9gCnIORuLJO3eoAcoEUEbzuzQMwtJkdxfCto_nbWci9NlduJz-A21GqBhUqY4WW7DpB7SHEaZ603qSr1VIZAKKF4grmNRbQoTFDadiaIg/https%3A%2F%2Fwww.instagram.com%2Funi_paderborn%2FUPB Facebook https://secure-web.cisco.com/1qI6cvPugysabKPf7WJIn-pK1ebwXTYqTkS1Cq7h9IJDbH45JWWj6sR0Z9sEoL4quEbX07iZINUBx5pniaPqbhosJj24-VIY4BpHAkXc6oUasQ_tzCxbLWIXIWQjUgn9xa_vhPo03M0iGQfqfJ7ifCcDo1PyIjbH6rPs0AnUrqTtrvmQgvXZNFWWC4oeWxJhD5KWLbgN1_3EsKJncd1K0EhGHQfA77txf7m8tnFdhqjJIwQWTVLQTCdDhZy8tznlMVmjM3Uybn95lN4g2UCElt6O3QsAnsIrqi2lfNPOGDtUKzu3CxamZULja1IYRO1H9lg4M_vq5pLlM-zq8v9gimA/https%3A%2F%2Fwww.facebook.com%2FunipaderbornHNI LinkedIn https://secure-web.cisco.com/1QjEIu8F4_OFs-qMy1zfRJ09N60yJv7f8jN4vl0JbHSAUaSFSGXgGeH482PZX2qdWXO7GHEoJGC5GaYv7YZtkeqnxY7aajLMHxnvxTSrQpCc9xHLlfVaAAbVpAMrZkEnitqEFRDuhr-YSCGPfz_y4r9S5kXKfKcL8DZOSkXoWOSZq4HYKGf-0biu-Ws1b5Lj6ezfevuVWceO6CqEmvI9XNsM6IMOGWP4PqVFubYsyTy9oD9OItISFKXHRtfN3DfMKAI5WDPUPkj7biO79nJLlaU50livW-AL6Ll100wOibeHQ7qSaxHHUug9nC95xoUIoBoKeqw2t6Nw5Ejr2VO4A5A/https%3A%2F%2Fwww.linkedin.com%2Fcompany%2F34889406HNI Twitter https://secure-web.cisco.com/1RiPhNxpWoH_W7GY4WC-7wEUB04OrzGVeskAVxjwYN9y6H1dRGOyDzXvzjdDwVvgF2TF5gAVBTzDI2DLA7PBb2Si3sg07spu1JQ0AGHbHwhgj3tqY-hy_eX0yDu2-vK10eCOnYHAHpJwnhNV_34-NvpPqchcT_Rp2MZNbOU-5AAePGFkMBcXyfXvyV9Zhwno3-IYnX5VM4sv0outdelfbpbJnx_6FDhesfkFxdc2nGFaFO3kTxTGi4SG9NKH7nQ3SgqRIOtUHc2KoMwcVYYdgWhcnJo4v3Es8EOoqyR_O5mSVg3e8t-6-ubuCiVVQml5ikA_2IHtD6rXhUZp5-FravA/https%3A%2F%2Ftwitter.com%2FHNI_PBHNI YouTube https://secure-web.cisco.com/11K2yPkMlVnMf6mztj9krvQ4gM44-jTlMplFJReirNNc8tb4x2EGOR8U6_gtK_IOSWCaiNZHcY5rQMOVNAS1TVEw_C8W-Be1sSwnGIv-6ROYuU5oOS9xU0z_dJR36JgFYbU6_u_LqLVldbvtGhQhCqJdkQSaWKkXn7ohs6wqA2eBcuMGnrrAmcovJ7YoMrz88O0z9s333srz_bgBgA2VHWBUivmBdoAIr4WtwdTDsmFGBmqVL4XRSrK3ydPju1wqmvRwizegoK-yiqJ2bvds0xZA8nTZKX16CiD9iCUhVBfus1LNlDY1WZQj8Gg24L7JoA5vqq3JAa0ttW44rKyj78w/https%3A%2F%2Fwww.youtube.com%2F%40HNIRedaktion
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Thank you for your quick answer! Could you please explain to me where to find the “stack1.mgh” file? In which part of the longitudinal analysis stream is it created? I thought it would be part of the fsaverage/surf folder, but I did not find it there. Looking into the individual BASE/surf folders I found the individual stack files after using “long_mris_slopes” tried to extract the individual values with mri_segstats --i subject_01_BASE/surf/lh.long.thickness-stack.mgh --seg perm.th40.abs.sig.ocn.mgh --avgwf subject_01.dat --sum subject_01.dat --excludeid 0 However, I am running into the following error: ERROR: dimension mismatch between input volume and seg input 132211 1 1 seg 163842 1 1
Did I understand something wrong? Do you have any idea how to fix this problem? Thank you in advance for your help!
Kind regards, Franziska Mund
________________________________ Von: Douglas N. Greve dgreve@mgh.harvard.edu Gesendet: Donnerstag, 31. Juli 2025 15:39:12 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Re: Individual pre- and post-values for cortical thickness after a paired analysis
Yes, you can run something like mri_segstats --i stack1.mgz --seg ocn.mgz --avgwf subject.vals1.dat --excludeid 0 --sum sum1.dat where stack1.mgz is the stack of subjects in fsaverage space from time point 1 The output subject.val1.dat will have a row for each subject and a column for each cluster. The value will be the average value from that subject over the voxels in that cluster
On 7/31/2025 9:26 AM, Franziska Mund wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
we have a longitudinal study design with one group and ran a paired analysis in FreeSurfer V6 (as described here: https://secure-web.cisco.com/1ifwXLM5pMomo96WQ1IwfCXwj7hatwd_Oh9BE0YWZXgI8rF...https://secure-web.cisco.com/1V0gSNyIvhCtX3j8K-mzIp_bu0OnK1ZDZxKlOeenlA2T-l0CCdlEjkvqSe_5KXnd2BsF6h2tMQlWydqH1m8dKAmoCEpn-TbkFaHJWOqGpSYtRU8YvMgQzcP2QDPVw3azcRBFW9C1XlQKk7m8bMYYozP3nmdcvhYw0JYyhHjkoxQOgcnd0zYH4S7XaSVtvWRFD4r_MjbvM8iG-0t0lmqJbYtixgRh3XHMAtobqfTEdgrqNk_fjPSL2M5iEDFemk9Hrlavuirl3qGaFh1WcfeX9q_SI8y8ZY4bIoYk8BnOINqrgvbl8EIJ2YvLhfqSqnz1c6lWT0TuWLUcnXChPRCK_YQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis). Afterwards we corrected for multiple comparisons (as described here: https://secure-web.cisco.com/17gpFIx8vHcBXq1usRrFPlTdH447uEb8K5jRKWgVb9rRJLJ...https://secure-web.cisco.com/1kF3xxriMcabTqMwlV5PjrV7Bz3-ihiWEkX08AlNLpslyHgUOXeF8fr5ulAvLPcyf8uMHq8hloj1Y0krgnu9ohcGi3EnBNppfRwRcB9TLq05apD-eGE0K0CzTmSAcVmw2etFiVP5PgwWAwPHUk7JIZrQVUVLi2EUia9T1UWuxO0p9FoioElKpdbAyBIeUJ7NH1O8Ihf4t4SWLnIDfP9Q5N_iL13R5ypa0TFVO14wZu8IhSGemg9TvCJHE2p5ES8a9ByJ1j715uelFLXsf_fr8VmOnWc-UAAujQ7EcU9n-yoDUBI_EAwXM5TAJJX57AVmv5Kmp850i96_x9yuV1H5kxw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0).
One cluster showed a significant change for cortical thickness and the average values of each subject were located in the “y.ocn.dat”.
However, we are now wondering how it is possible to get the individual pre- and post-values for that specific cluster for all subjects. Is there any method to do so?
Any assistance is very much appreciated!
Thanks in advance.
Best,
Franziska
Dr. Franziska Mund
Wissenschaftliche Mitarbeiterin
Sportmedizinisches Institut
[cid:part1.0iNDn2A0.PU07wjwp@mgh.harvard.edu]http://secure-web.cisco.com/1MXBasQV5Cu2ljjndrv0cARnfi2yk8RGCa8zldfWWltrJ-clKDp1TTmfgdmfpvcpEmQNX54gc28scyHnZ8M-2BDH3Dlzzf_fn_QsAuoyUmMhJ7pOL9xb4B69Y5y8D83CQr3FH5l3lKzASZsyjcVSjjqUTHCqkgvoTIWub1BG-zcTu3uRYMn53q2PxCtR41BYuKpQ3wjhlrm0nbXsRyCgbus6JIQcveVKXuTs5YG560jEDWli-Su624hwo9w2uyA9uA7m9Eh0lYAlxcbrAn1-tgPwVII9Jag6mbD7E9kUE7p9Q2XLHs023yZj9Xhiny4hX/http%3A%2F%2Fwww.upb.de%2F
Warburger Straße 100
33098 Paderborn
Raum SP.0.508
Telefon +49 5251 60-3187
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The "stack1" is your stack of subjects from time point 1. Generally, this is created with a call to mris_preproc
On 8/1/2025 9:03 AM, Franziska Mund wrote:
External Email - Use Caution
Thank you for your quick answer!
Could you please explain to me where to find the “stack1.mgh” file? In which part of the longitudinal analysis stream is it created? I thought it would be part of the fsaverage/surf folder, but I did not find it there.
Looking into the individual BASE/surf folders I found the individual stack files after using “long_mris_slopes” tried to extract the individual values with
/mri_segstats --i subject_01_BASE/surf/lh.long.thickness-stack.mgh --seg perm.th40.abs.sig.ocn.mgh --avgwf subject_01.dat --sum subject_01.dat --excludeid 0/
However, I am running into the following error:
ERROR: dimension mismatch between input volume and seg
input 132211 1 1
seg163842 1 1
Did I understand something wrong? Do you have any idea how to fix this problem?
Thank you in advance for your help!
Kind regards,
Franziska Mund
*Von:* Douglas N. Greve dgreve@mgh.harvard.edu *Gesendet:* Donnerstag, 31. Juli 2025 15:39:12 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* [Freesurfer] Re: Individual pre- and post-values for cortical thickness after a paired analysis Yes, you can run something like mri_segstats --i stack1.mgz --seg ocn.mgz --avgwf subject.vals1.dat --excludeid 0 --sum sum1.dat where stack1.mgz is the stack of subjects in fsaverage space from time point 1 The output subject.val1.dat will have a row for each subject and a column for each cluster. The value will be the average value from that subject over the voxels in that cluster
On 7/31/2025 9:26 AM, Franziska Mund wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
we have a longitudinal study design with one group and ran a paired analysis in FreeSurfer V6 (as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis https://secure-web.cisco.com/1V0gSNyIvhCtX3j8K-mzIp_bu0OnK1ZDZxKlOeenlA2T-l0CCdlEjkvqSe_5KXnd2BsF6h2tMQlWydqH1m8dKAmoCEpn-TbkFaHJWOqGpSYtRU8YvMgQzcP2QDPVw3azcRBFW9C1XlQKk7m8bMYYozP3nmdcvhYw0JYyhHjkoxQOgcnd0zYH4S7XaSVtvWRFD4r_MjbvM8iG-0t0lmqJbYtixgRh3XHMAtobqfTEdgrqNk_fjPSL2M5iEDFemk9Hrlavuirl3qGaFh1WcfeX9q_SI8y8ZY4bIoYk8BnOINqrgvbl8EIJ2YvLhfqSqnz1c6lWT0TuWLUcnXChPRCK_YQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis). Afterwards we corrected for multiple comparisons (as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0 https://secure-web.cisco.com/1kF3xxriMcabTqMwlV5PjrV7Bz3-ihiWEkX08AlNLpslyHgUOXeF8fr5ulAvLPcyf8uMHq8hloj1Y0krgnu9ohcGi3EnBNppfRwRcB9TLq05apD-eGE0K0CzTmSAcVmw2etFiVP5PgwWAwPHUk7JIZrQVUVLi2EUia9T1UWuxO0p9FoioElKpdbAyBIeUJ7NH1O8Ihf4t4SWLnIDfP9Q5N_iL13R5ypa0TFVO14wZu8IhSGemg9TvCJHE2p5ES8a9ByJ1j715uelFLXsf_fr8VmOnWc-UAAujQ7EcU9n-yoDUBI_EAwXM5TAJJX57AVmv5Kmp850i96_x9yuV1H5kxw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0).
One cluster showed a significant change for cortical thickness and the average values of each subject were located in the “y.ocn.dat”.
However, we are now wondering how it is possible to get the individual pre- and post-values for that specific cluster for all subjects. Is there any method to do so?
Any assistance is very much appreciated!
Thanks in advance.
Best,
Franziska
*Dr. Franziska Mund *
Wissenschaftliche Mitarbeiterin
Sportmedizinisches Institut
Warburger Straße 100
33098 Paderborn
*Raum*SP.0.508
*Telefon*+49 5251 60-3187
*Mail*mund@sportmed.uni-paderborn.de mailto:mund@sportmed.uni-paderborn.de
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Again, thank you so much for your help! I was able to extract the values and compute the difference manually. However, the calculated difference is slightly different than the output/values in the “y.ocn.dat” file for the significant cluster. Do you have any idea where this may come from?
________________________________ Von: Douglas N. Greve dgreve@mgh.harvard.edu Gesendet: Sonntag, 3. August 2025 22:39:57 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Re: Individual pre- and post-values for cortical thickness after a paired analysis
The "stack1" is your stack of subjects from time point 1. Generally, this is created with a call to mris_preproc
On 8/1/2025 9:03 AM, Franziska Mund wrote:
External Email - Use Caution Thank you for your quick answer! Could you please explain to me where to find the “stack1.mgh” file? In which part of the longitudinal analysis stream is it created? I thought it would be part of the fsaverage/surf folder, but I did not find it there. Looking into the individual BASE/surf folders I found the individual stack files after using “long_mris_slopes” tried to extract the individual values with mri_segstats --i subject_01_BASE/surf/lh.long.thickness-stack.mgh --seg perm.th40.abs.sig.ocn.mgh --avgwf subject_01.dat --sum subject_01.dat --excludeid 0 However, I am running into the following error: ERROR: dimension mismatch between input volume and seg input 132211 1 1 seg 163842 1 1
Did I understand something wrong? Do you have any idea how to fix this problem? Thank you in advance for your help!
Kind regards, Franziska Mund
________________________________ Von: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Gesendet: Donnerstag, 31. Juli 2025 15:39:12 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Re: Individual pre- and post-values for cortical thickness after a paired analysis
Yes, you can run something like mri_segstats --i stack1.mgz --seg ocn.mgz --avgwf subject.vals1.dat --excludeid 0 --sum sum1.dat where stack1.mgz is the stack of subjects in fsaverage space from time point 1 The output subject.val1.dat will have a row for each subject and a column for each cluster. The value will be the average value from that subject over the voxels in that cluster
On 7/31/2025 9:26 AM, Franziska Mund wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
we have a longitudinal study design with one group and ran a paired analysis in FreeSurfer V6 (as described here: https://secure-web.cisco.com/1Kt-aJ3k0e6w1pfHNWV7Ld_PthmlG42ZsjUrkeN0XTJN6_c...https://secure-web.cisco.com/1V0gSNyIvhCtX3j8K-mzIp_bu0OnK1ZDZxKlOeenlA2T-l0CCdlEjkvqSe_5KXnd2BsF6h2tMQlWydqH1m8dKAmoCEpn-TbkFaHJWOqGpSYtRU8YvMgQzcP2QDPVw3azcRBFW9C1XlQKk7m8bMYYozP3nmdcvhYw0JYyhHjkoxQOgcnd0zYH4S7XaSVtvWRFD4r_MjbvM8iG-0t0lmqJbYtixgRh3XHMAtobqfTEdgrqNk_fjPSL2M5iEDFemk9Hrlavuirl3qGaFh1WcfeX9q_SI8y8ZY4bIoYk8BnOINqrgvbl8EIJ2YvLhfqSqnz1c6lWT0TuWLUcnXChPRCK_YQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis). Afterwards we corrected for multiple comparisons (as described here: https://secure-web.cisco.com/1wtzw3yO073EIHXoQcUGAcoqKScm172hBJtmDHr-udtOVHD...https://secure-web.cisco.com/1kF3xxriMcabTqMwlV5PjrV7Bz3-ihiWEkX08AlNLpslyHgUOXeF8fr5ulAvLPcyf8uMHq8hloj1Y0krgnu9ohcGi3EnBNppfRwRcB9TLq05apD-eGE0K0CzTmSAcVmw2etFiVP5PgwWAwPHUk7JIZrQVUVLi2EUia9T1UWuxO0p9FoioElKpdbAyBIeUJ7NH1O8Ihf4t4SWLnIDfP9Q5N_iL13R5ypa0TFVO14wZu8IhSGemg9TvCJHE2p5ES8a9ByJ1j715uelFLXsf_fr8VmOnWc-UAAujQ7EcU9n-yoDUBI_EAwXM5TAJJX57AVmv5Kmp850i96_x9yuV1H5kxw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0).
One cluster showed a significant change for cortical thickness and the average values of each subject were located in the “y.ocn.dat”.
However, we are now wondering how it is possible to get the individual pre- and post-values for that specific cluster for all subjects. Is there any method to do so?
Any assistance is very much appreciated!
Thanks in advance.
Best,
Franziska
Dr. Franziska Mund
Wissenschaftliche Mitarbeiterin
Sportmedizinisches Institut
[cid:part1.5jmOysLO.9oXSkVPO@mgh.harvard.edu]http://secure-web.cisco.com/1MXBasQV5Cu2ljjndrv0cARnfi2yk8RGCa8zldfWWltrJ-clKDp1TTmfgdmfpvcpEmQNX54gc28scyHnZ8M-2BDH3Dlzzf_fn_QsAuoyUmMhJ7pOL9xb4B69Y5y8D83CQr3FH5l3lKzASZsyjcVSjjqUTHCqkgvoTIWub1BG-zcTu3uRYMn53q2PxCtR41BYuKpQ3wjhlrm0nbXsRyCgbus6JIQcveVKXuTs5YG560jEDWli-Su624hwo9w2uyA9uA7m9Eh0lYAlxcbrAn1-tgPwVII9Jag6mbD7E9kUE7p9Q2XLHs023yZj9Xhiny4hX/http%3A%2F%2Fwww.upb.de%2F
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33098 Paderborn
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Telefon +49 5251 60-3187
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I found the mistake and now the values are identical. Thanks so much for the help! ________________________________ Von: Franziska Mund mund@sportmed.uni-paderborn.de Gesendet: Dienstag, 5. August 2025 18:39:52 An: Freesurfer support list Betreff: [Freesurfer] Re: Individual pre- and post-values for cortical thickness after a paired analysis
External Email - Use Caution Again, thank you so much for your help! I was able to extract the values and compute the difference manually. However, the calculated difference is slightly different than the output/values in the “y.ocn.dat” file for the significant cluster. Do you have any idea where this may come from?
________________________________ Von: Douglas N. Greve dgreve@mgh.harvard.edu Gesendet: Sonntag, 3. August 2025 22:39:57 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Re: Individual pre- and post-values for cortical thickness after a paired analysis
The "stack1" is your stack of subjects from time point 1. Generally, this is created with a call to mris_preproc
On 8/1/2025 9:03 AM, Franziska Mund wrote:
External Email - Use Caution Thank you for your quick answer! Could you please explain to me where to find the “stack1.mgh” file? In which part of the longitudinal analysis stream is it created? I thought it would be part of the fsaverage/surf folder, but I did not find it there. Looking into the individual BASE/surf folders I found the individual stack files after using “long_mris_slopes” tried to extract the individual values with mri_segstats --i subject_01_BASE/surf/lh.long.thickness-stack.mgh --seg perm.th40.abs.sig.ocn.mgh --avgwf subject_01.dat --sum subject_01.dat --excludeid 0 However, I am running into the following error: ERROR: dimension mismatch between input volume and seg input 132211 1 1 seg 163842 1 1
Did I understand something wrong? Do you have any idea how to fix this problem? Thank you in advance for your help!
Kind regards, Franziska Mund
________________________________ Von: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Gesendet: Donnerstag, 31. Juli 2025 15:39:12 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Re: Individual pre- and post-values for cortical thickness after a paired analysis
Yes, you can run something like mri_segstats --i stack1.mgz --seg ocn.mgz --avgwf subject.vals1.dat --excludeid 0 --sum sum1.dat where stack1.mgz is the stack of subjects in fsaverage space from time point 1 The output subject.val1.dat will have a row for each subject and a column for each cluster. The value will be the average value from that subject over the voxels in that cluster
On 7/31/2025 9:26 AM, Franziska Mund wrote:
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Dear FreeSurfer Developers,
we have a longitudinal study design with one group and ran a paired analysis in FreeSurfer V6 (as described here: https://secure-web.cisco.com/1WAo0LB7f9qcqCDbQGka9OjrF5psOUmMTxA-0K7jU_cgnqL...https://secure-web.cisco.com/1V0gSNyIvhCtX3j8K-mzIp_bu0OnK1ZDZxKlOeenlA2T-l0CCdlEjkvqSe_5KXnd2BsF6h2tMQlWydqH1m8dKAmoCEpn-TbkFaHJWOqGpSYtRU8YvMgQzcP2QDPVw3azcRBFW9C1XlQKk7m8bMYYozP3nmdcvhYw0JYyhHjkoxQOgcnd0zYH4S7XaSVtvWRFD4r_MjbvM8iG-0t0lmqJbYtixgRh3XHMAtobqfTEdgrqNk_fjPSL2M5iEDFemk9Hrlavuirl3qGaFh1WcfeX9q_SI8y8ZY4bIoYk8BnOINqrgvbl8EIJ2YvLhfqSqnz1c6lWT0TuWLUcnXChPRCK_YQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis). Afterwards we corrected for multiple comparisons (as described here: https://secure-web.cisco.com/11LcI0RkWc_e6-Vmg-cFO-UvedEVvAvmtpbZ35bzIefx0-J...https://secure-web.cisco.com/1kF3xxriMcabTqMwlV5PjrV7Bz3-ihiWEkX08AlNLpslyHgUOXeF8fr5ulAvLPcyf8uMHq8hloj1Y0krgnu9ohcGi3EnBNppfRwRcB9TLq05apD-eGE0K0CzTmSAcVmw2etFiVP5PgwWAwPHUk7JIZrQVUVLi2EUia9T1UWuxO0p9FoioElKpdbAyBIeUJ7NH1O8Ihf4t4SWLnIDfP9Q5N_iL13R5ypa0TFVO14wZu8IhSGemg9TvCJHE2p5ES8a9ByJ1j715uelFLXsf_fr8VmOnWc-UAAujQ7EcU9n-yoDUBI_EAwXM5TAJJX57AVmv5Kmp850i96_x9yuV1H5kxw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0).
One cluster showed a significant change for cortical thickness and the average values of each subject were located in the “y.ocn.dat”.
However, we are now wondering how it is possible to get the individual pre- and post-values for that specific cluster for all subjects. Is there any method to do so?
Any assistance is very much appreciated!
Thanks in advance.
Best,
Franziska
Dr. Franziska Mund
Wissenschaftliche Mitarbeiterin
Sportmedizinisches Institut
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Douglas N. Greve -
Franziska Mund