Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
Sure, any simulation can’t be exhaustive, but my understanding, chatting with Anderson, is that their 2014 paper simulated a quite large space of designs and Freedman-Lane is appropriate for the vast majority of the GLMs that we would encounter in neuroimaging. Also, again per Anderson, I believe that method implemented in mri_glmfit-sim is that of Manly for those interested in linking what mri_glmfit-sim is doing to the results in Winkler (e.g., Table 7). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 8/30/16, 8:33 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: By "wrong" I meant that permutation no longer gives exact p-values in expectation with non-orthogonal designs. There is no theory to characterize the accuracy of Freeman-Lane of the other methods. In this sense, they are not approximations but ad hoc methods that people hope do a better job than parametric methods. Anderson tested them on a wide range of designs, but it was, of course, not exhaustive. The accuracy of his results may not extend to other designs, so it is a buyer-beware situation (as with all neuroimaging). On 8/29/16 10:16 PM, Harms, Michael wrote: > Hi, > I wouldn’t say that non-orthogonal designs are “wrong” to use with > permutation. Rather, there are different approaches to handling that > situation and produce approximate p-values. See Table 2 in Winkler’s >2014 > paper, and the results therein comparing the various approaches: > > http://www.ncbi.nlm.nih.gov/pubmed/24530839 > > > PALM actually gives you control over the method used, with the default > (and recommended) approach being that of “Freedman-Lane", which is the > same approach used by FSL’s ‘randomise’ tool to handle correlated > covariates. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110Email: mha...@wustl.edu > > > > > On 8/29/16, 7:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Matt Glasser" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > m...@ma-tea.com> wrote: > > PALM handles GIFTI and CIFTI data. > > Peace, > > Matt. > > On 8/29/16, 6:21 PM, "Douglas N Greve" > <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > gr...@nmr.mgh.harvard.edu> wrote: > >> Does PALM do surface-based? Also, there is no way to appropriately >> handle this. For permutation, non-orthogonal designs are wrong. There >> are ways to try to compensate for it, which is what PALM is doing. Sorry >> to be nit-picky! >> >> >> On 08/29/2016 06:12 PM, Harms, Michael wrote: >>> Hi Maaike, >>> Why not just use PALM? Then you don¹t have to worry about this (since >>> PALM appropriately handles the situation of correlated covariates). >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> >>> --- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave.Tel: 314-747-6173 >>> St. Louis, MO 63110Email: mha...@wustl.edu >>> >>> >>> >>> >>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>> of >>> Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >>> gr...@nmr.mgh.harvard.edu> wrote: >>> >>> It is hard to say. Since the subjects are not exchangeable, the >>> permutation is technically not appropriate. Check the winkler paper, I >>> think he talks about what happens if you just don't do anything. >>> >>> >>> On 08/29/2016 11:07 AM, maaike rive wrote: >>>> Hi all, >>>> >>>> >>>> Is using forced permutation for non-orthogonal design matrices wrong >>>> or is it allowed to do this instead of using tools like palm (what >>>> happens eg with the covariates when using forced permutation)? I >>>> used forced permutat
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
>>> of > >>> Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > >>> gr...@nmr.mgh.harvard.edu> wrote: > >>> > >>> It is hard to say. Since the subjects are not exchangeable, the > >>> permutation is technically not appropriate. Check the winkler paper, I > >>> think he talks about what happens if you just don't do anything. > >>> > >>> > >>> On 08/29/2016 11:07 AM, maaike rive wrote: > >>>> Hi all, > >>>> > >>>> > >>>> Is using forced permutation for non-orthogonal design matrices wrong > >>>> or is it allowed to do this instead of using tools like palm (what > >>>> happens eg with the covariates when using forced permutation)? I > >>>> used forced permutation and it seemed to work, results were (partly) > >>>> comparable to what I found with monte carlo simulations. > >>>> > >>>> > >>>> Thanks, Maaike > >>>> > >>>> > >>>> > > >>>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu > >>>> <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael > >>>> <mha...@wustl.edu> > >>>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13 > >>>> *Aan:* Freesurfer support list > >>>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing > >>>> running after 3 days! > >>>> > >>>> Hi, > >>>> You might want to check out FSL¹s PALM tool, which has a bit more > >>>> sophisticated permutation framework, and allows for permutation in the > >>>> context of non-orthogonal covariates. > >>>> > >>>> cheers, > >>>> -MH > >>>> > >>>> -- > >>>> Michael Harms, Ph.D. > >>>> --- > >>>> Conte Center for the Neuroscience of Mental Disorders > >>>> Washington University School of Medicine > >>>> Department of Psychiatry, Box 8134 > >>>> 660 South Euclid Ave.Tel: 314-747-6173 > >>>> St. Louis, MO 63110Email: mha...@wustl.edu > >>>> > >>>> From: <freesurfer-boun...@nmr.mgh.harvard.edu > >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay > >>>> Kurani <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> > >>>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>>> Date: Thursday, August 25, 2016 at 4:13 PM > >>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>>> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running > >>>> after 3 days! > >>>> > >>>> Hi Doug, > >>>> Thanks for the help! I think I figured out the issue based on > your > >>>> response. > >>>> 1) I created a template to use for this group and named it fsaverage > >>>> (including creating monte carlo simulations) for simplicity of > >>>> integrating with freesurfer as I am newer to it. This is why the > >>>> sizes didn't match up as you expected > >>>> but the mri_glmfit still ran. > >>>> > >>>> 2) I deleted the folder and restarted without background processes. > >>>> The error became apparent. Of my covariates (2 fix factors and 3 > >>>> quantitative), not all were orthogonal. In looking at the error more, > >>>> it seems that i need to add the > >>>> --perm-force if I wanted the simulation to run, however the background > >>>> processes were not aware of this error and kept polling as you > >>>> mentioned. > >>>> > >>>> This brings me to a new but related issue. From what I have read in > >>>> other freesurfer posts, it is statistically incorrect to use > >>>> --perm-force for non-orthogonal covariates (or continuous covariates). > >>>> I am unsure how to proceed. > >>>> a) If I ran permutation testing (to overcome the issue of incorrect > >>>> smoothness estimations fro
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
By "wrong" I meant that permutation no longer gives exact p-values in expectation with non-orthogonal designs. There is no theory to characterize the accuracy of Freeman-Lane of the other methods. In this sense, they are not approximations but ad hoc methods that people hope do a better job than parametric methods. Anderson tested them on a wide range of designs, but it was, of course, not exhaustive. The accuracy of his results may not extend to other designs, so it is a buyer-beware situation (as with all neuroimaging). On 8/29/16 10:16 PM, Harms, Michael wrote: > Hi, > I wouldn’t say that non-orthogonal designs are “wrong” to use with > permutation. Rather, there are different approaches to handling that > situation and produce approximate p-values. See Table 2 in Winkler’s 2014 > paper, and the results therein comparing the various approaches: > > http://www.ncbi.nlm.nih.gov/pubmed/24530839 > > > PALM actually gives you control over the method used, with the default > (and recommended) approach being that of “Freedman-Lane", which is the > same approach used by FSL’s ‘randomise’ tool to handle correlated > covariates. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110Email: mha...@wustl.edu > > > > > On 8/29/16, 7:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Matt Glasser" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > m...@ma-tea.com> wrote: > > PALM handles GIFTI and CIFTI data. > > Peace, > > Matt. > > On 8/29/16, 6:21 PM, "Douglas N Greve" > <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > gr...@nmr.mgh.harvard.edu> wrote: > >> Does PALM do surface-based? Also, there is no way to appropriately >> handle this. For permutation, non-orthogonal designs are wrong. There >> are ways to try to compensate for it, which is what PALM is doing. Sorry >> to be nit-picky! >> >> >> On 08/29/2016 06:12 PM, Harms, Michael wrote: >>> Hi Maaike, >>> Why not just use PALM? Then you don¹t have to worry about this (since >>> PALM appropriately handles the situation of correlated covariates). >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> >>> --- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave.Tel: 314-747-6173 >>> St. Louis, MO 63110Email: mha...@wustl.edu >>> >>> >>> >>> >>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>> of >>> Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >>> gr...@nmr.mgh.harvard.edu> wrote: >>> >>> It is hard to say. Since the subjects are not exchangeable, the >>> permutation is technically not appropriate. Check the winkler paper, I >>> think he talks about what happens if you just don't do anything. >>> >>> >>> On 08/29/2016 11:07 AM, maaike rive wrote: >>>> Hi all, >>>> >>>> >>>> Is using forced permutation for non-orthogonal design matrices wrong >>>> or is it allowed to do this instead of using tools like palm (what >>>> happens eg with the covariates when using forced permutation)? I >>>> used forced permutation and it seemed to work, results were (partly) >>>> comparable to what I found with monte carlo simulations. >>>> >>>> >>>> Thanks, Maaike >>>> >>>> >>>> >>>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu >>>> <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael >>>> <mha...@wustl.edu> >>>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13 >>>> *Aan:* Freesurfer support list >>>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing >>>> running after 3 days! >>>> >>>> Hi, >>>> You might want to check out FSL¹s PALM tool, which has a bit more >>>> sophisticated permutation framework, and allows for permutation in the >>>&g
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
Hi, I wouldn’t say that non-orthogonal designs are “wrong” to use with permutation. Rather, there are different approaches to handling that situation and produce approximate p-values. See Table 2 in Winkler’s 2014 paper, and the results therein comparing the various approaches: http://www.ncbi.nlm.nih.gov/pubmed/24530839 PALM actually gives you control over the method used, with the default (and recommended) approach being that of “Freedman-Lane", which is the same approach used by FSL’s ‘randomise’ tool to handle correlated covariates. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 8/29/16, 7:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Matt Glasser" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of m...@ma-tea.com> wrote: PALM handles GIFTI and CIFTI data. Peace, Matt. On 8/29/16, 6:21 PM, "Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >Does PALM do surface-based? Also, there is no way to appropriately >handle this. For permutation, non-orthogonal designs are wrong. There >are ways to try to compensate for it, which is what PALM is doing. Sorry >to be nit-picky! > > >On 08/29/2016 06:12 PM, Harms, Michael wrote: >> Hi Maaike, >> Why not just use PALM? Then you don¹t have to worry about this (since >> PALM appropriately handles the situation of correlated covariates). >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave.Tel: 314-747-6173 >> St. Louis, MO 63110Email: mha...@wustl.edu >> >> >> >> >> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>of >> Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> gr...@nmr.mgh.harvard.edu> wrote: >> >> It is hard to say. Since the subjects are not exchangeable, the >> permutation is technically not appropriate. Check the winkler paper, I >> think he talks about what happens if you just don't do anything. >> >> >> On 08/29/2016 11:07 AM, maaike rive wrote: >>> Hi all, >>> >>> >>> Is using forced permutation for non-orthogonal design matrices wrong >>> or is it allowed to do this instead of using tools like palm (what >>> happens eg with the covariates when using forced permutation)? I >>> used forced permutation and it seemed to work, results were (partly) >>> comparable to what I found with monte carlo simulations. >>> >>> >>> Thanks, Maaike >>> >>> >>>---- >>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael >>> <mha...@wustl.edu> >>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13 >>> *Aan:* Freesurfer support list >>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing >>> running after 3 days! >>> >>> Hi, >>> You might want to check out FSL¹s PALM tool, which has a bit more >>> sophisticated permutation framework, and allows for permutation in the >>> context of non-orthogonal covariates. >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> --- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave.Tel: 314-747-6173 >>> St. Louis, MO 63110Email: mha...@wustl.edu >>> >>> From: <freesurfer-boun...@nmr.mgh.harvard.edu >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay >>> Kurani <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> >>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Date: Thursday, August 25, 2016 at 4:13 PM >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>> <mailto:free
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
PALM handles GIFTI and CIFTI data. Peace, Matt. On 8/29/16, 6:21 PM, "Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >Does PALM do surface-based? Also, there is no way to appropriately >handle this. For permutation, non-orthogonal designs are wrong. There >are ways to try to compensate for it, which is what PALM is doing. Sorry >to be nit-picky! > > >On 08/29/2016 06:12 PM, Harms, Michael wrote: >> Hi Maaike, >> Why not just use PALM? Then you don¹t have to worry about this (since >> PALM appropriately handles the situation of correlated covariates). >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave.Tel: 314-747-6173 >> St. Louis, MO 63110Email: mha...@wustl.edu >> >> >> >> >> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>of >> Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> gr...@nmr.mgh.harvard.edu> wrote: >> >> It is hard to say. Since the subjects are not exchangeable, the >> permutation is technically not appropriate. Check the winkler paper, I >> think he talks about what happens if you just don't do anything. >> >> >> On 08/29/2016 11:07 AM, maaike rive wrote: >>> Hi all, >>> >>> >>> Is using forced permutation for non-orthogonal design matrices wrong >>> or is it allowed to do this instead of using tools like palm (what >>> happens eg with the covariates when using forced permutation)? I >>> used forced permutation and it seemed to work, results were (partly) >>> comparable to what I found with monte carlo simulations. >>> >>> >>> Thanks, Maaike >>> >>> >>>------------ >>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael >>> <mha...@wustl.edu> >>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13 >>> *Aan:* Freesurfer support list >>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing >>> running after 3 days! >>> >>> Hi, >>> You might want to check out FSL¹s PALM tool, which has a bit more >>> sophisticated permutation framework, and allows for permutation in the >>> context of non-orthogonal covariates. >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> --- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave.Tel: 314-747-6173 >>> St. Louis, MO 63110Email: mha...@wustl.edu >>> >>> From: <freesurfer-boun...@nmr.mgh.harvard.edu >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay >>> Kurani <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> >>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Date: Thursday, August 25, 2016 at 4:13 PM >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running >>> after 3 days! >>> >>> Hi Doug, >>> Thanks for the help! I think I figured out the issue based on your >>> response. >>> 1) I created a template to use for this group and named it fsaverage >>> (including creating monte carlo simulations) for simplicity of >>> integrating with freesurfer as I am newer to it. This is why the >>> sizes didn't match up as you expected >>> but the mri_glmfit still ran. >>> >>> 2) I deleted the folder and restarted without background processes. >>> The error became apparent. Of my covariates (2 fix factors and 3 >>> quantitative), not all were orthogonal. In looking at the error more, >>> it seems that i need to add the >>> --perm-force if I wanted the simulation to run, however the background >>> processes were not aw
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
Does PALM do surface-based? Also, there is no way to appropriately handle this. For permutation, non-orthogonal designs are wrong. There are ways to try to compensate for it, which is what PALM is doing. Sorry to be nit-picky! On 08/29/2016 06:12 PM, Harms, Michael wrote: > Hi Maaike, > Why not just use PALM? Then you don’t have to worry about this (since > PALM appropriately handles the situation of correlated covariates). > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110Email: mha...@wustl.edu > > > > > On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > gr...@nmr.mgh.harvard.edu> wrote: > > It is hard to say. Since the subjects are not exchangeable, the > permutation is technically not appropriate. Check the winkler paper, I > think he talks about what happens if you just don't do anything. > > > On 08/29/2016 11:07 AM, maaike rive wrote: >> Hi all, >> >> >> Is using forced permutation for non-orthogonal design matrices wrong >> or is it allowed to do this instead of using tools like palm (what >> happens eg with the covariates when using forced permutation)? I >> used forced permutation and it seemed to work, results were (partly) >> comparable to what I found with monte carlo simulations. >> >> >> Thanks, Maaike >> >> >> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael >> <mha...@wustl.edu> >> *Verzonden:* vrijdag 26 augustus 2016 01:00:13 >> *Aan:* Freesurfer support list >> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing >> running after 3 days! >> >> Hi, >> You might want to check out FSL’s PALM tool, which has a bit more >> sophisticated permutation framework, and allows for permutation in the >> context of non-orthogonal covariates. >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave.Tel: 314-747-6173 >> St. Louis, MO 63110Email: mha...@wustl.edu >> >> From: <freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay >> Kurani <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> >> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Date: Thursday, August 25, 2016 at 4:13 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running >> after 3 days! >> >> Hi Doug, >> Thanks for the help! I think I figured out the issue based on your >> response. >> 1) I created a template to use for this group and named it fsaverage >> (including creating monte carlo simulations) for simplicity of >> integrating with freesurfer as I am newer to it. This is why the >> sizes didn't match up as you expected >> but the mri_glmfit still ran. >> >> 2) I deleted the folder and restarted without background processes. >> The error became apparent. Of my covariates (2 fix factors and 3 >> quantitative), not all were orthogonal. In looking at the error more, >> it seems that i need to add the >> --perm-force if I wanted the simulation to run, however the background >> processes were not aware of this error and kept polling as you mentioned. >> >> This brings me to a new but related issue. From what I have read in >> other freesurfer posts, it is statistically incorrect to use >> --perm-force for non-orthogonal covariates (or continuous covariates). >> I am unsure how to proceed. >> a) If I ran permutation testing (to overcome the issue of incorrect >> smoothness estimations from the gaussian distribution assumption), >> then I run into the issue of non-orthogonal covariates. Is there a >> way to orthogonalize the data in >> free
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
Hi Maaike, Why not just use PALM? Then you don’t have to worry about this (since PALM appropriately handles the situation of correlated covariates). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: It is hard to say. Since the subjects are not exchangeable, the permutation is technically not appropriate. Check the winkler paper, I think he talks about what happens if you just don't do anything. On 08/29/2016 11:07 AM, maaike rive wrote: > > Hi all, > > > Is using forced permutation for non-orthogonal design matrices wrong > or is it allowed to do this instead of using tools like palm (what > happens eg with the covariates when using forced permutation)? I > used forced permutation and it seemed to work, results were (partly) > comparable to what I found with monte carlo simulations. > > > Thanks, Maaike > > > *Van:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael > <mha...@wustl.edu> > *Verzonden:* vrijdag 26 augustus 2016 01:00:13 > *Aan:* Freesurfer support list > *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing > running after 3 days! > > Hi, > You might want to check out FSL’s PALM tool, which has a bit more > sophisticated permutation framework, and allows for permutation in the > context of non-orthogonal covariates. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110Email: mha...@wustl.edu > > From: <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay > Kurani <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, August 25, 2016 at 4:13 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running > after 3 days! > > Hi Doug, >Thanks for the help! I think I figured out the issue based on your > response. > 1) I created a template to use for this group and named it fsaverage > (including creating monte carlo simulations) for simplicity of > integrating with freesurfer as I am newer to it. This is why the > sizes didn't match up as you expected > but the mri_glmfit still ran. > > 2) I deleted the folder and restarted without background processes. > The error became apparent. Of my covariates (2 fix factors and 3 > quantitative), not all were orthogonal. In looking at the error more, > it seems that i need to add the > --perm-force if I wanted the simulation to run, however the background > processes were not aware of this error and kept polling as you mentioned. > > This brings me to a new but related issue. From what I have read in > other freesurfer posts, it is statistically incorrect to use > --perm-force for non-orthogonal covariates (or continuous covariates). > I am unsure how to proceed. > a) If I ran permutation testing (to overcome the issue of incorrect > smoothness estimations from the gaussian distribution assumption), > then I run into the issue of non-orthogonal covariates. Is there a > way to orthogonalize the data in > freesurfer, or a solution to this issue? > > b) If orthogonalizing is difficult to implement, another option is > running Qdec with the montecarlo simulation at a more conservative p > value (p< 0.001). From your previous posts, the testing at this p > value for 10mm seems to meet the 5% FPR. One question is if the > non-orthogonal data affects this analysis as well for this model? > > Thanks, > Ajay > > On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani > <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> wrote: > > Hi Freesurfer Experts, >I am trying to use freesurfer's mri_glmfit-sim tool to run > permutation testing on cor
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
It is hard to say. Since the subjects are not exchangeable, the permutation is technically not appropriate. Check the winkler paper, I think he talks about what happens if you just don't do anything. On 08/29/2016 11:07 AM, maaike rive wrote: > > Hi all, > > > Is using forced permutation for non-orthogonal design matrices wrong > or is it allowed to do this instead of using tools like palm (what > happens eg with the covariates when using forced permutation)? I > used forced permutation and it seemed to work, results were (partly) > comparable to what I found with monte carlo simulations. > > > Thanks, Maaike > > > *Van:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael > <mha...@wustl.edu> > *Verzonden:* vrijdag 26 augustus 2016 01:00:13 > *Aan:* Freesurfer support list > *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing > running after 3 days! > > Hi, > You might want to check out FSL’s PALM tool, which has a bit more > sophisticated permutation framework, and allows for permutation in the > context of non-orthogonal covariates. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110Email: mha...@wustl.edu > > From: <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay > Kurani <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, August 25, 2016 at 4:13 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running > after 3 days! > > Hi Doug, >Thanks for the help! I think I figured out the issue based on your > response. > 1) I created a template to use for this group and named it fsaverage > (including creating monte carlo simulations) for simplicity of > integrating with freesurfer as I am newer to it. This is why the > sizes didn't match up as you expected > but the mri_glmfit still ran. > > 2) I deleted the folder and restarted without background processes. > The error became apparent. Of my covariates (2 fix factors and 3 > quantitative), not all were orthogonal. In looking at the error more, > it seems that i need to add the > --perm-force if I wanted the simulation to run, however the background > processes were not aware of this error and kept polling as you mentioned. > > This brings me to a new but related issue. From what I have read in > other freesurfer posts, it is statistically incorrect to use > --perm-force for non-orthogonal covariates (or continuous covariates). > I am unsure how to proceed. > a) If I ran permutation testing (to overcome the issue of incorrect > smoothness estimations from the gaussian distribution assumption), > then I run into the issue of non-orthogonal covariates. Is there a > way to orthogonalize the data in > freesurfer, or a solution to this issue? > > b) If orthogonalizing is difficult to implement, another option is > running Qdec with the montecarlo simulation at a more conservative p > value (p< 0.001). From your previous posts, the testing at this p > value for 10mm seems to meet the 5% FPR. One question is if the > non-orthogonal data affects this analysis as well for this model? > > Thanks, > Ajay > > On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani > <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> wrote: > > Hi Freesurfer Experts, >I am trying to use freesurfer's mri_glmfit-sim tool to run > permutation testing on cortical thickness data (as recommended by > Doug in my previous post: > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html > > <http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html> > ) > > Most of the tutorials I found were not related to permutation > testing so the subsequent steps may be incorrect. Please let me > know where I go wrong... > > 1) I first ran QDec to generate a folder for the analysis which > would create the subsequent fsgd and y files needed my > mri_
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
Hi all, Is using forced permutation for non-orthogonal design matrices wrong or is it allowed to do this instead of using tools like palm (what happens eg with the covariates when using forced permutation)? I used forced permutation and it seemed to work, results were (partly) comparable to what I found with monte carlo simulations. Thanks, Maaike Van: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael <mha...@wustl.edu> Verzonden: vrijdag 26 augustus 2016 01:00:13 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days! Hi, You might want to check out FSL’s PALM tool, which has a bit more sophisticated permutation framework, and allows for permutation in the context of non-orthogonal covariates. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay Kurani <dr.ajay.kur...@gmail.com<mailto:dr.ajay.kur...@gmail.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, August 25, 2016 at 4:13 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days! Hi Doug, Thanks for the help! I think I figured out the issue based on your response. 1) I created a template to use for this group and named it fsaverage (including creating monte carlo simulations) for simplicity of integrating with freesurfer as I am newer to it. This is why the sizes didn't match up as you expected but the mri_glmfit still ran. 2) I deleted the folder and restarted without background processes. The error became apparent. Of my covariates (2 fix factors and 3 quantitative), not all were orthogonal. In looking at the error more, it seems that i need to add the --perm-force if I wanted the simulation to run, however the background processes were not aware of this error and kept polling as you mentioned. This brings me to a new but related issue. From what I have read in other freesurfer posts, it is statistically incorrect to use --perm-force for non-orthogonal covariates (or continuous covariates). I am unsure how to proceed. a) If I ran permutation testing (to overcome the issue of incorrect smoothness estimations from the gaussian distribution assumption), then I run into the issue of non-orthogonal covariates. Is there a way to orthogonalize the data in freesurfer, or a solution to this issue? b) If orthogonalizing is difficult to implement, another option is running Qdec with the montecarlo simulation at a more conservative p value (p< 0.001). From your previous posts, the testing at this p value for 10mm seems to meet the 5% FPR. One question is if the non-orthogonal data affects this analysis as well for this model? Thanks, Ajay On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com<mailto:dr.ajay.kur...@gmail.com>> wrote: Hi Freesurfer Experts, I am trying to use freesurfer's mri_glmfit-sim tool to run permutation testing on cortical thickness data (as recommended by Doug in my previous post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html ) Most of the tutorials I found were not related to permutation testing so the subsequent steps may be incorrect. Please let me know where I go wrong... 1) I first ran QDec to generate a folder for the analysis which would create the subsequent fsgd and y files needed my mri_glmfit-sim. I am running both left and right hemisphere cortical thickness analysis with 10mm smoothing. The following is for just the left hemisphere. Note I am doing a 3 group comparison, but for this 2 group ttest I manually centered the data based on the 3 group mean for age and education. 2) I ran the following command: /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 1 2 perm.abs.2 --sim-sign abs --bg 16 Prior to running the command above, from the y.fsdg file I deleted the fwhm estimate of 13mm since this was not correctly estimated (ACF with long tails). I assumed that by removing this estimate, it would force the permutation test to calculate based on the data but when looking at the log output I see the following which says fwhm 0: cmdline mri_glmfit.bin --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
Something strange is going on in your data. You are using fsaverage, but the size of the data in PDvsMCI_lh_thickness_10mm/y.mgh does not match (it has 148278 vertices, not 163842 of fsaverage). This is causing the processes to die, but the backgrounding software does not know that the process died and so just keeps polling. What I don't understand is why the original call to mri_glmfit did not die too. When I run it as such, it does die. It may be that the data in that folder did not get deleted by QDEC, and there is a strange mix of data in there. Can you delete that folder and try it again? Also, don't run it in background mode until you know that it is working. On 08/25/2016 01:18 PM, Ajay Kurani wrote: > Hi Freesurfer Experts, >I am trying to use freesurfer's mri_glmfit-sim tool to run > permutation testing on cortical thickness data (as recommended by Doug > in my previous post: > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html > ) > > Most of the tutorials I found were not related to permutation testing > so the subsequent steps may be incorrect. Please let me know where I > go wrong... > > 1) I first ran QDec to generate a folder for the analysis which would > create the subsequent fsgd and y files needed my mri_glmfit-sim. I am > running both left and right hemisphere cortical thickness analysis > with 10mm smoothing. The following is for just the left hemisphere. > Note I am doing a 3 group comparison, but for this 2 group ttest I > manually centered the data based on the 3 group mean for age and > education. > > 2) I ran the following command: > /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 1 > 2 perm.abs.2 --sim-sign abs --bg 16 > > Prior to running the command above, from the y.fsdg file I deleted the > fwhm estimate of 13mm since this was not correctly estimated (ACF with > long tails). I assumed that by removing this estimate, it would force > the permutation test to calculate based on the data but when looking > at the log output I see the following which says fwhm 0: > > cmdline mri_glmfit.bin --C > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx > > --C > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Female-Intercept-thickness.mtx > > --C > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx > > --C > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group-Intercept-thickness.mtx > > --sim perm 625 2 ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 --y > /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh > --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm 0 > --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage lh > white --sim-done > ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013 > > 3)I started this a few days ago on a 16 core machine and it is still > running in the terminal. I have 150 subjects in the analysis and > specified 1 iterations. In the terminal I assumed when I reach > Poll 1 it would be complete but currently I am at : Poll 13341 job > 1 Thu Aug 25 12:03:51 CDT 2016 > > Questions: > a) I am curious, is this going to run 10,000 simulations X 150 > patients or does the Poll number not have anything to do with the > number of iterations it is on? > > > b) Did I run this procedure correctly? Was I incorrect in deleting > the fwhm estimate from y.fsgd file generated by Qdec even though we > know the estimate is incorrect since smoothness assumed a gaussian > distribution as opposed to gaussian with heavy tails > > c) I noticed in the logfile the following warning: > INFO: gd2mtx_method is dods > Computing normalized matrix > Normalized matrix condition is 5.65727 > Matrix condition is 935.597 > Found 136777 voxels in mask > Reshaping mriglm->mask... > search space = 89675.729228 > ERROR: design matrix is not orthogonal, cannot be used with permutation. > If this something you really want to do, run with --perm-force > Poll 2 job 1 Tue Aug 23 22:58:18 CDT 2016 > > I am not sure if this means my simulation is incorrect? > > Thanks, > Ajay > > > ___ > 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
Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!
Can you tar up the glmdir and drop it to me at our filedrop (link below)? Also,what version of FS are you using? Also, can you try running it without backgrounding on a few (say, 100) iterations to see if it completes? Then try with backgrounding (problem may be backgrounding) On 08/25/2016 01:18 PM, Ajay Kurani wrote: > Hi Freesurfer Experts, >I am trying to use freesurfer's mri_glmfit-sim tool to run > permutation testing on cortical thickness data (as recommended by Doug > in my previous post: > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html > ) > > Most of the tutorials I found were not related to permutation testing > so the subsequent steps may be incorrect. Please let me know where I > go wrong... > > 1) I first ran QDec to generate a folder for the analysis which would > create the subsequent fsgd and y files needed my mri_glmfit-sim. I am > running both left and right hemisphere cortical thickness analysis > with 10mm smoothing. The following is for just the left hemisphere. > Note I am doing a 3 group comparison, but for this 2 group ttest I > manually centered the data based on the 3 group mean for age and > education. > > 2) I ran the following command: > /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 1 > 2 perm.abs.2 --sim-sign abs --bg 16 > > Prior to running the command above, from the y.fsdg file I deleted the > fwhm estimate of 13mm since this was not correctly estimated (ACF with > long tails). I assumed that by removing this estimate, it would force > the permutation test to calculate based on the data but when looking > at the log output I see the following which says fwhm 0: > > cmdline mri_glmfit.bin --C > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx > > --C > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Female-Intercept-thickness.mtx > > --C > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx > > --C > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group-Intercept-thickness.mtx > > --sim perm 625 2 ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 --y > /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh > --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm 0 > --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage lh > white --sim-done > ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013 > > 3)I started this a few days ago on a 16 core machine and it is still > running in the terminal. I have 150 subjects in the analysis and > specified 1 iterations. In the terminal I assumed when I reach > Poll 1 it would be complete but currently I am at : Poll 13341 job > 1 Thu Aug 25 12:03:51 CDT 2016 > > Questions: > a) I am curious, is this going to run 10,000 simulations X 150 > patients or does the Poll number not have anything to do with the > number of iterations it is on? > > > b) Did I run this procedure correctly? Was I incorrect in deleting > the fwhm estimate from y.fsgd file generated by Qdec even though we > know the estimate is incorrect since smoothness assumed a gaussian > distribution as opposed to gaussian with heavy tails > > c) I noticed in the logfile the following warning: > INFO: gd2mtx_method is dods > Computing normalized matrix > Normalized matrix condition is 5.65727 > Matrix condition is 935.597 > Found 136777 voxels in mask > Reshaping mriglm->mask... > search space = 89675.729228 > ERROR: design matrix is not orthogonal, cannot be used with permutation. > If this something you really want to do, run with --perm-force > Poll 2 job 1 Tue Aug 23 22:58:18 CDT 2016 > > I am not sure if this means my simulation is incorrect? > > Thanks, > Ajay > > > ___ > 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] mri_glmfit-sim permutation testing running after 3 days!
Hi Freesurfer Experts, I am trying to use freesurfer's mri_glmfit-sim tool to run permutation testing on cortical thickness data (as recommended by Doug in my previous post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html ) Most of the tutorials I found were not related to permutation testing so the subsequent steps may be incorrect. Please let me know where I go wrong... 1) I first ran QDec to generate a folder for the analysis which would create the subsequent fsgd and y files needed my mri_glmfit-sim. I am running both left and right hemisphere cortical thickness analysis with 10mm smoothing. The following is for just the left hemisphere. Note I am doing a 3 group comparison, but for this 2 group ttest I manually centered the data based on the 3 group mean for age and education. 2) I ran the following command: /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 1 2 perm.abs.2 --sim-sign abs --bg 16 Prior to running the command above, from the y.fsdg file I deleted the fwhm estimate of 13mm since this was not correctly estimated (ACF with long tails). I assumed that by removing this estimate, it would force the permutation test to calculate based on the data but when looking at the log output I see the following which says fwhm 0: cmdline mri_glmfit.bin --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Female-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group-Intercept-thickness.mtx --sim perm 625 2 ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 --y /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm 0 --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage lh white --sim-done ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013 3)I started this a few days ago on a 16 core machine and it is still running in the terminal. I have 150 subjects in the analysis and specified 1 iterations. In the terminal I assumed when I reach Poll 1 it would be complete but currently I am at : Poll 13341 job 1 Thu Aug 25 12:03:51 CDT 2016 Questions: a) I am curious, is this going to run 10,000 simulations X 150 patients or does the Poll number not have anything to do with the number of iterations it is on? b) Did I run this procedure correctly? Was I incorrect in deleting the fwhm estimate from y.fsgd file generated by Qdec even though we know the estimate is incorrect since smoothness assumed a gaussian distribution as opposed to gaussian with heavy tails c) I noticed in the logfile the following warning: INFO: gd2mtx_method is dods Computing normalized matrix Normalized matrix condition is 5.65727 Matrix condition is 935.597 Found 136777 voxels in mask Reshaping mriglm->mask... search space = 89675.729228 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force Poll 2 job 1 Tue Aug 23 22:58:18 CDT 2016 I am not sure if this means my simulation is incorrect? Thanks, Ajay ___ 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.
