Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
That is what I thought. For version 6, I have a work-around which you might be able to use with version 5. Copy these files ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_ldanaflac.m ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/flac_conmat.m to $FREESURFER_HOME/fsfast/toolbox (make backups of the ones that are already there). Then create a file for your contrast in the folder created by mkanalysis-sess (eg, yourcontrast.mtx). Note the mtx ending and not .mat ending. This is a text file with the contrast that you want. I would suggest making a contrast that replicates one of the other contrasts you made with mkcontrast-sess to assure that you have it right. doug On 11/13/2014 06:42 PM, Caspar M. Schwiedrzik wrote: ok, so the issue is in fast_ldanaflac.m, around line 520: flac.con(nthcon).ContrastMtx_0=[]; that effectively ignores the contrasts that are set up in mystudy. caspar 2014-11-13 17:33 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, so I made contrast matrices and stored them in mystudy, and then ran selxavg3-sess per subject. I defined three different contrasts (in three mat files), but selxacg3-sess only gives me one analysis, it seems to be an F-test. When I do isxconcat-sess after that, I get six ces files per analysis (I presume one for each of my predictors), not three (number of contrasts). Is there a way for me to force selxavg3-sess to actually compute the contrasts that I want? Thanks, Caspar 2014-11-13 12:16 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: I don't know whether that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works. On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote: Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar 2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu: Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar 2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu mailto:b...@cs.wisc.edu: Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
I don't know whether that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works. On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote: Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar 2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu: Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Hi Doug, so I made contrast matrices and stored them in mystudy, and then ran selxavg3-sess per subject. I defined three different contrasts (in three mat files), but selxacg3-sess only gives me one analysis, it seems to be an F-test. When I do isxconcat-sess after that, I get six ces files per analysis (I presume one for each of my predictors), not three (number of contrasts). Is there a way for me to force selxavg3-sess to actually compute the contrasts that I want? Thanks, Caspar 2014-11-13 12:16 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: I don't know whether that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works. On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote: Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar 2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu: Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
ok, so the issue is in fast_ldanaflac.m, around line 520: flac.con(nthcon).ContrastMtx_0=[]; that effectively ignores the contrasts that are set up in mystudy. caspar 2014-11-13 17:33 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : Hi Doug, so I made contrast matrices and stored them in mystudy, and then ran selxavg3-sess per subject. I defined three different contrasts (in three mat files), but selxacg3-sess only gives me one analysis, it seems to be an F-test. When I do isxconcat-sess after that, I get six ces files per analysis (I presume one for each of my predictors), not three (number of contrasts). Is there a way for me to force selxavg3-sess to actually compute the contrasts that I want? Thanks, Caspar 2014-11-13 12:16 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: I don't know whether that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works. On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote: Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar 2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu mailto:b...@cs.wisc.edu: Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime?
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? 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 gr...@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu: Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto: cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar ___ Freesurfer mailing list
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu mailto:b...@cs.wisc.edu: Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu mailto:b...@cs.wisc.edu: Sorry, Though we do have freesurfer pipelines we run in Madison, I responded to wrong email. Bill Taylor Center for High Throughput Computing Computer Sciences University of Wisconsin, Madison On 11/11/2014 12:09 PM, Bill Taylor wrote: I'll start the process thursday. On 11/11/2014 12:04 PM, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Actually, you can still do each contrast individually. Each will produce ces and cesvar files. Take the difference between the ces files and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? 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 gr...@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.
Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST
Hi Doug, thanks for your reply. I would like to feed the differences into a FFX group analysis, so I think I will need to resort to your workaround. It would be great if you could provide that. Thanks! Caspar 2014-11-10 13:45 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: To get sig maps for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up: I have a taskreg file with 6 continuous predictors. I would like to run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6). From what I gather, selxavg3-sess will run automatic contrasts on taskregs, but the automatic contrasts are against baseline. This is not what I need at this point. mk-contrast-sess does not like what I am putting in because I do not have a paradigm file in which condition numbers are specified. Is there a way to compute specific contrasts between multiple taskregs, and if not, is there a workaround? Thank you very much, Caspar 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu mailto:cschwie...@rockefeller.edu: Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? 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 gr...@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Running a contrast on multiple taskregs in FSFAST
Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5? Thanks, Caspar ___ 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.
