[Freesurfer] mergecontrasts-sess command not found
External Email - Use Caution Hi Freesurfers, I’m trying to use mergecontrasts-sess to merge two contrasts of an analysis, but I get this: mergecontrasts-sess: Command not found. I tried with other Fs-Fast commands and they work. I am running on a Ubuntu 18.04, 64 bit. I downloaded the 6.0.0. Freesurfer version from the official page. Could you help me? Thanks a lot Paula ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Help with mergecontrasts-sess function
External Email - Use Caution Dear experts, I am running an fMRI experiment in which I have four conditions: two main conditions (condition A and condition B) and two respective control conditions (condition Acontrol and condition Bcontrol). I would like to create a map showing significantly greater activity for condition A relative to condition B, after subtracting out the activity for the respective control conditions. In other words, I would like to perform the following contrast: (condition A - condition A control) - (condition B - condition B control) Then I would like to have a map that shows the reverse contrast too:(condition B - condition B control) - (condition A - condition A control). How do I do that?To obtain the first map: (condition A - condition A control) - (condition B - condition B control) I have tried with the mergecontrasts-sess function with the -conjunction flag and the OR option as detailed below: mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh where Contrast1= (condition A - condition A control) and Contrast2= (condition B - condition B control) however the map I get is exactly the same as (condition A - condition A control), as if subtracting out Contrast 2 had no impact on the map. Thanks, Paula ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help with mergecontrasts-sess function
External Email - Use Caution Thanks for your reply, that worked. Can you please tell me where I can find a summary table of the activated regions resulting from the conjunction analysis? Best regards, Paula > Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve > ha scritto: > > You would just run mkcontrast-sess, eg, if your four conditions are > ordered condA, condAcontrol, condB, condBcont, then > mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 > -a 4 > If you want it reversed, then just reverse the a's and c's > > On 10/23/2020 4:39 AM, Paula Maldonado wrote: >> External Email - Use Caution >> >> Dear experts, >> I am running an fMRI experiment in which I have four conditions: two main >> conditions (condition A and condition B) and two respective control >> conditions (condition Acontrol and condition Bcontrol). >> I would like to create a map showing significantly greater activity for >> condition A relative to condition B, after subtracting out the activity for >> the respective control conditions. In other words, I would like to perform >> the following contrast: >> (condition A - condition A control) - (condition B - condition B control) >> Then I would like to have a map that shows the reverse contrast >> too:(condition B - condition B control) - (condition A - condition A >> control). >> >> How do I do that?To obtain the first map: (condition A - condition A >> control) - (condition B - condition B control) I have tried with the >> mergecontrasts-sess function with the -conjunction flag and the OR option as >> detailed below: >> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis >> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 >> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh >> >> where Contrast1= (condition A - condition A control) and Contrast2= >> (condition B - condition B control) >> however the map I get is exactly the same as (condition A - condition A >> control), as if subtracting out Contrast 2 had no impact on the map. >> >> Thanks, >> >> Paula >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1PFjXV9QuzlqX9EM-0nPOfUdZYLQSATBLC8FqlNjXq7jjSAZPsriNuFC5cBdszxFTkbLeK41STuJh8SXf1PJHh9AjhfEdCAFxmFKjNrK061xASObgXwPRx0XAaC3UV_7L8XAj5nYl6mfw-6OFG58jxAfIBowfOUq9nGIedyp1bZty7Tx2EoVU1UyiAtUliIHMD8enigzVsOO6xo7LnoBmsQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1PFjXV9QuzlqX9EM-0nPOfUdZYLQSATBLC8FqlNjXq7jjSAZPsriNuFC5cBdszxFTkbLeK41STuJh8SXf1PJHh9AjhfEdCAFxmFKjNrK061xASObgXwPRx0XAaC3UV_7L8XAj5nYl6mfw-6OFG58jxAfIBowfOUq9nGIedyp1bZty7Tx2EoVU1UyiAtUliIHMD8enigzVsOO6xo7LnoBmsQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}
External Email - Use Caution Yes, please, Best regards, Paula > Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve > ha scritto: > > There is not a summary table, it is just a map. Do you want a cluster table? > > On 11/10/2020 11:26 AM, Paula Maldonado wrote: >> External Email - Use Caution >> >> Thanks for your reply, that worked. Can you please tell me where I can find >> a summary table of the activated regions resulting from the conjunction >> analysis? >> >> Best regards, >> >> Paula >> >> >> >> >>> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve >>> mailto:dgr...@mgh.harvard.edu>> ha scritto: >>> >>> You would just run mkcontrast-sess, eg, if your four conditions are >>> ordered condA, condAcontrol, condB, condBcont, then >>> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 >>> -a 4 >>> If you want it reversed, then just reverse the a's and c's >>> >>> On 10/23/2020 4:39 AM, Paula Maldonado wrote: >>>> External Email - Use Caution >>>> >>>> Dear experts, >>>> I am running an fMRI experiment in which I have four conditions: two main >>>> conditions (condition A and condition B) and two respective control >>>> conditions (condition Acontrol and condition Bcontrol). >>>> I would like to create a map showing significantly greater activity for >>>> condition A relative to condition B, after subtracting out the activity >>>> for the respective control conditions. In other words, I would like to >>>> perform the following contrast: >>>> (condition A - condition A control) - (condition B - condition B control) >>>> Then I would like to have a map that shows the reverse contrast >>>> too:(condition B - condition B control) - (condition A - condition A >>>> control). >>>> >>>> How do I do that?To obtain the first map: (condition A - condition A >>>> control) - (condition B - condition B control) I have tried with the >>>> mergecontrasts-sess function with the -conjunction flag and the OR option >>>> as detailed below: >>>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis >>>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 >>>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh >>>> >>>> where Contrast1= (condition A - condition A control) and Contrast2= >>>> (condition B - condition B control) >>>> however the map I get is exactly the same as (condition A - condition A >>>> control), as if subtracting out Contrast 2 had no impact on the map. >>>> >>>> Thanks, >>>> >>>> Paula >>>> >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://secure-web.cisco.com/1Z2tGDyQNcpsepFLH1RpzlNDQxc_6IY6IIhtT02Fixl08uKeAj23rFY8-89HPPtInUYDnYy-rra956-G_gKTe2vgUEUcozRaB5NEcYattZo5uJygrWTgwZ7Ll5oz2Fj1NfitZig2r6W59F8YCgtxgsT3cMJybWH_v4UF-BKr4mwQktK4mQc_CMjSfCvVHiue3knd4ddLTqkfgYdduLYUaz_bUOkNnglGmTm93JmdWpTfvAztsE_SWpGwKhohR0NT87t1wPOyYFF7yqMc_dc_9oA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> <https://secure-web.cisco.com/1Z2tGDyQNcpsepFLH1RpzlNDQxc_6IY6IIhtT02Fixl08uKeAj23rFY8-89HPPtInUYDnYy-rra956-G_gKTe2vgUEUcozRaB5NEcYattZo5uJygrWTgwZ7Ll5oz2Fj1NfitZig2r6W59F8YCgtxgsT3cMJybWH_v4UF-BKr4mwQktK4mQc_CMjSfCvVHiue3knd4ddLTqkfgYdduLYUaz_bUOkNnglGmTm93JmdWpTfvAztsE_SWpGwKhohR0NT87t1wPOyYFF7yqMc_dc_9oA/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> >>> https://secure-web.cisco.com/1Z2tGDyQNcpsepFLH1RpzlNDQxc_6IY6IIhtT02Fixl08uKeAj23rFY8-89HPPtInUYDnYy-rra956-G_gKTe2vgUEUcozRaB5NEcYattZo5uJygrWTgwZ7Ll5oz2Fj1NfitZig2r6W59F8YCgtxgsT3cMJybWH_v4UF-BKr4mwQktK4mQc_CMjSfCvVHiue3knd4ddLTqkfgYdduLYUaz_bUOkNnglGmTm93JmdWpTfvAztsE_SWpGwKhohR0NT87t1wPOyYFF7yqMc_dc_9oA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <https://secure-web.cisco.com/1Z2tGDyQNcpsepFLH1RpzlNDQxc_6IY6IIhtT02Fixl08uKeAj23rFY8-89HPPtInUYDnYy-rra
Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}
External Email - Use Caution Dear Douglas, Could you please tell me where can I find the cluster table? Thank you, Best regards, Paula > Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve > ha scritto: > > There is not a summary table, it is just a map. Do you want a cluster table? > > On 11/10/2020 11:26 AM, Paula Maldonado wrote: >> External Email - Use Caution >> >> Thanks for your reply, that worked. Can you please tell me where I can find >> a summary table of the activated regions resulting from the conjunction >> analysis? >> >> Best regards, >> >> Paula >> >> >> >> >>> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve >>> mailto:dgr...@mgh.harvard.edu>> ha scritto: >>> >>> You would just run mkcontrast-sess, eg, if your four conditions are >>> ordered condA, condAcontrol, condB, condBcont, then >>> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 >>> -a 4 >>> If you want it reversed, then just reverse the a's and c's >>> >>> On 10/23/2020 4:39 AM, Paula Maldonado wrote: >>>> External Email - Use Caution >>>> >>>> Dear experts, >>>> I am running an fMRI experiment in which I have four conditions: two main >>>> conditions (condition A and condition B) and two respective control >>>> conditions (condition Acontrol and condition Bcontrol). >>>> I would like to create a map showing significantly greater activity for >>>> condition A relative to condition B, after subtracting out the activity >>>> for the respective control conditions. In other words, I would like to >>>> perform the following contrast: >>>> (condition A - condition A control) - (condition B - condition B control) >>>> Then I would like to have a map that shows the reverse contrast >>>> too:(condition B - condition B control) - (condition A - condition A >>>> control). >>>> >>>> How do I do that?To obtain the first map: (condition A - condition A >>>> control) - (condition B - condition B control) I have tried with the >>>> mergecontrasts-sess function with the -conjunction flag and the OR option >>>> as detailed below: >>>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis >>>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 >>>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh >>>> >>>> where Contrast1= (condition A - condition A control) and Contrast2= >>>> (condition B - condition B control) >>>> however the map I get is exactly the same as (condition A - condition A >>>> control), as if subtracting out Contrast 2 had no impact on the map. >>>> >>>> Thanks, >>>> >>>> Paula >>>> >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://secure-web.cisco.com/1MSoNZugOE7aA1gOT7VibT4hmgT8729NyDyuSI5M_XIIJSHN9Oa6mpnmC2hkuFPGXkj7yukLmsGUfZBLZlQdYsY2AxtcrFwTAUaJit7RnSO-H3GPvE9U-FUvEA1D-EbOKM7OhgHOgL7846L6UgEhe81mVpJtl2L3sDGDBm7MSG4ChljHVJ517sv6mBgstQqHkHndzlu186P6Y6HoLybv0FzehRXKGA7DUFTgNZ2LwQfBNW5QeulsSuRIGiB3wlK4H99pjN1XyQPXgV5XCwCSaKg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> <https://secure-web.cisco.com/1MSoNZugOE7aA1gOT7VibT4hmgT8729NyDyuSI5M_XIIJSHN9Oa6mpnmC2hkuFPGXkj7yukLmsGUfZBLZlQdYsY2AxtcrFwTAUaJit7RnSO-H3GPvE9U-FUvEA1D-EbOKM7OhgHOgL7846L6UgEhe81mVpJtl2L3sDGDBm7MSG4ChljHVJ517sv6mBgstQqHkHndzlu186P6Y6HoLybv0FzehRXKGA7DUFTgNZ2LwQfBNW5QeulsSuRIGiB3wlK4H99pjN1XyQPXgV5XCwCSaKg/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> >>> https://secure-web.cisco.com/1MSoNZugOE7aA1gOT7VibT4hmgT8729NyDyuSI5M_XIIJSHN9Oa6mpnmC2hkuFPGXkj7yukLmsGUfZBLZlQdYsY2AxtcrFwTAUaJit7RnSO-H3GPvE9U-FUvEA1D-EbOKM7OhgHOgL7846L6UgEhe81mVpJtl2L3sDGDBm7MSG4ChljHVJ517sv6mBgstQqHkHndzlu186P6Y6HoLybv0FzehRXKGA7DUFTgNZ2LwQfBNW5QeulsSuRIGiB3wlK4H99pjN1XyQPXgV5XCwCSaKg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fm
Re: [Freesurfer] Help with mergecontrasts-sess function
External Email - Use Caution Thanks for your reply, However I have now a doubt regarding one aspect that I had not noticed before. What I wanted to do is to perform the contrast (condA>condAcontrol)>(condB>condBcontrol) with the order of my condition being condA, condAcontrol, condB, condBcontrol You said that to do so I should use -a 1 -c 2 -c 3 -a 4, but I don’t understand why condition 3 is -c and condition 4 is -a. To my understanding a is assigning a positive weight to my predictors, while c is assigning a negative one. So if I run -a 1 -c 2 -c 3 -a 4, am I not testing the contrast (condA>condAcontrol)>(condBcontrol>condB) ? In addition, if now I want to obtain: (condA>condB)>(condAcontrol>condBcontrol) should I run mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 3 -c 2 -a 4, or -a 1 -c 3 -a 2 -c 4? Thanks, Paula > Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve > ha scritto: > > You would just run mkcontrast-sess, eg, if your four conditions are > ordered condA, condAcontrol, condB, condBcont, then > mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 > -a 4 > If you want it reversed, then just reverse the a's and c's > > On 10/23/2020 4:39 AM, Paula Maldonado wrote: >> External Email - Use Caution >> >> Dear experts, >> I am running an fMRI experiment in which I have four conditions: two main >> conditions (condition A and condition B) and two respective control >> conditions (condition Acontrol and condition Bcontrol). >> I would like to create a map showing significantly greater activity for >> condition A relative to condition B, after subtracting out the activity for >> the respective control conditions. In other words, I would like to perform >> the following contrast: >> (condition A - condition A control) - (condition B - condition B control) >> Then I would like to have a map that shows the reverse contrast >> too:(condition B - condition B control) - (condition A - condition A >> control). >> >> How do I do that?To obtain the first map: (condition A - condition A >> control) - (condition B - condition B control) I have tried with the >> mergecontrasts-sess function with the -conjunction flag and the OR option as >> detailed below: >> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis >> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 >> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh >> >> where Contrast1= (condition A - condition A control) and Contrast2= >> (condition B - condition B control) >> however the map I get is exactly the same as (condition A - condition A >> control), as if subtracting out Contrast 2 had no impact on the map. >> >> Thanks, >> >> Paula >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/17Vis7CsewfzKVGLwUV1wLKkghjPfiDm9VeIZ6t9CHXifdcWEg0Z6PdDLO-bFcp-Ie-E_CNaHQm97ldOW3j0GgaivIZZogL1rmUpS07_zswoVI7F_x8z4aL9RkBExxoEMbJjuSwOQiY-xoGtoLQF6kQVRq4Z8YJ64IlUuxvRM0j1FALZF5_BxMy_IxGa0P5vezrjvpHsK9T76iLBmck0BFNQKuOxWjhK1p-dQGxmCPkdVOP_18BUraanTnU6tG93o_F4dSSNY678vxXeomHj0sQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/17Vis7CsewfzKVGLwUV1wLKkghjPfiDm9VeIZ6t9CHXifdcWEg0Z6PdDLO-bFcp-Ie-E_CNaHQm97ldOW3j0GgaivIZZogL1rmUpS07_zswoVI7F_x8z4aL9RkBExxoEMbJjuSwOQiY-xoGtoLQF6kQVRq4Z8YJ64IlUuxvRM0j1FALZF5_BxMy_IxGa0P5vezrjvpHsK9T76iLBmck0BFNQKuOxWjhK1p-dQGxmCPkdVOP_18BUraanTnU6tG93o_F4dSSNY678vxXeomHj0sQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
