Did you down load all the files in the patch? I think the new mri_surfcluster is there
On 4/8/2020 8:51 AM, s7675854@stud.uni-frankfurt.de wrote:
External Email - Use Caution Hi again, I already took a few more steps and set up PALM/ fspalm. It's working fine, up to the point where it does the actual cluster analysis. As part of the script, the command mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject fsaverage --hemi lh --annot aparc --sum resilience. clustertable.summary --no-fixmni --surf white --ocn resilience.ocn.mgz oannot ./resilience.ocn.annot --sig2pmax --bonferroni-max2 is generated. However, the last two flags (--sig2pmax --bonferroni-max2) are not recognized, so it crashes. Indeed, they do not appear as possible flags in the mri_surfcluster --help section, so how and why do they get here...? Just to see what happens, I ran the mri_surfcluster... command without the last 2 flags, which only gave me another error: "could not read fsp_clustere_tstat_fwep.mgz as type"
Do you have an idea what I could do about this? Thanks a lot, Doro
Zitat von s7675854@rz.uni-frankfurt.de:
Hi Douglas,
I just saw that permutation wasn't working for me because I use continuous covariates/ a non-orthogonal design. You just answered to a similar question in the mailing list yesterday and suggested to add "--perm-resid", but this flag does not exist for the mri_glmfit-sim command, does it? Do I have to install PALM to be able to run permutation on my design or is there any way around that?
Thanks again,
Doro Zitat von "Douglas N. Greve" dgreve@mgh.harvard.edu:
On 4/6/2020 10:57 AM, s7675854@stud.uni-frankfurt.de wrote:
External Email - Use Caution Hi Douglas,
thanks a lot for your quick response. I wanted to use Monte Carlo sim as all other analyses in our project include a monte carlo simulation and I try to keep things consistent. Am I getting you right - there is no way to run a monte carlo simulation with LGI data? And why exactly would you not recommend it in this case (even if it worked)?
Yes, you can do the MCZ simulation yourself with mri_mcsim, something like mri_mcsim --o /your/space/mcsim/fsaverage/lh/cortex --base mc-z --save-iter --surf fsaverage lh --nreps 1000 --fwhm 37 Then run mri_glmfit-sim as you did before, but specify --mczsim-dir /your/space/mcsim
I did try permutations with freesurfer in the past, but it never really worked out for me, to be honest. They kept running for ages and I stopped them after 6-7 days...
Not sure what happened, but if you want to debug it, I can help
Thanks in advance,
Doro Zitat von "Douglas N. Greve" dgreve@mgh.harvard.edu:
The problem is that mri_glmfit-sim is looking for a entry in the table that does not exist. The table only goes up to a smoothness level of 35. LGI data tend to bed very smooth. I would strongly recommend that you use permutation instead. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...
On 4/6/2020 7:42 AM, s7675854@stud.uni-frankfurt.de wrote:
External Email - Use Caution Dear Freesurfer experts,
I'm trying to run a simulation (--> mri_glmfit-sim) with cached LGI data (fwhm10), but get an error due to the estimated fwhm kernel. The folder corresponding to the fwhm value (-->37) does not exist, I guess because it's a pretty unusual value...?
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 36.855100 ERROR: cannot find /apps/prod/x86_64/freesurfer-6.0.1/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/abs/th20/mc-z.csd
I've seen mails describing similar issues in the archive and from your explanation I more or less understand that you cannot define this value as it is estimated in the process...? However, I did not see if there is a solution to this problem. What could I do about it now?
I attached the logfiles and would be very grateful for your help,
thanks a lot and stay healthy,
Doro
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi,
I did, but if this is a new version it probably co-exists with the old mri_surfcluster in my PATH (I am working on a server and am not allowed to delete files there..hmm). Why do the two flags (--sig2pmax and --bonferroni-max2) not appear in the mri_surfcluster guide (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster)? Is there a new version of the command description as well?
Thanks a lot and happy easter,
doro
Zitat von "Douglas N. Greve" dgreve@mgh.harvard.edu:
Did you down load all the files in the patch? I think the new mri_surfcluster is there
On 4/8/2020 8:51 AM, s7675854@stud.uni-frankfurt.de wrote:
External Email - Use Caution Hi again, I already took a few more steps and set up PALM/ fspalm. It's working fine, up to the point where it does the actual cluster analysis. As part of the script, the command mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject fsaverage --hemi lh --annot aparc --sum resilience. clustertable.summary --no-fixmni --surf white --ocn resilience.ocn.mgz oannot ./resilience.ocn.annot --sig2pmax --bonferroni-max2 is generated. However, the last two flags (--sig2pmax --bonferroni-max2) are not recognized, so it crashes. Indeed, they do not appear as possible flags in the mri_surfcluster --help section, so how and why do they get here...? Just to see what happens, I ran the mri_surfcluster... command without the last 2 flags, which only gave me another error: "could not read fsp_clustere_tstat_fwep.mgz as type"
Do you have an idea what I could do about this? Thanks a lot, Doro
Zitat von s7675854@rz.uni-frankfurt.de:
Hi Douglas,
I just saw that permutation wasn't working for me because I use continuous covariates/ a non-orthogonal design. You just answered to a similar question in the mailing list yesterday and suggested to add "--perm-resid", but this flag does not exist for the mri_glmfit-sim command, does it? Do I have to install PALM to be able to run permutation on my design or is there any way around that?
Thanks again,
Doro Zitat von "Douglas N. Greve" dgreve@mgh.harvard.edu:
On 4/6/2020 10:57 AM, s7675854@stud.uni-frankfurt.de wrote:
External Email - Use Caution Hi Douglas,
thanks a lot for your quick response. I wanted to use Monte Carlo sim as all other analyses in our project include a monte carlo simulation and I try to keep things consistent. Am I getting you right - there is no way to run a monte carlo simulation with LGI data? And why exactly would you not recommend it in this case (even if it worked)?
Yes, you can do the MCZ simulation yourself with mri_mcsim, something like mri_mcsim --o /your/space/mcsim/fsaverage/lh/cortex --base mc-z --save-iter --surf fsaverage lh --nreps 1000 --fwhm 37 Then run mri_glmfit-sim as you did before, but specify --mczsim-dir /your/space/mcsim
I did try permutations with freesurfer in the past, but it never really worked out for me, to be honest. They kept running for ages and I stopped them after 6-7 days...
Not sure what happened, but if you want to debug it, I can help
Thanks in advance,
Doro Zitat von "Douglas N. Greve" dgreve@mgh.harvard.edu:
The problem is that mri_glmfit-sim is looking for a entry in the table that does not exist. The table only goes up to a smoothness level of 35. LGI data tend to bed very smooth. I would strongly recommend that you use permutation instead. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0... On 4/6/2020 7:42 AM, s7675854@stud.uni-frankfurt.de wrote: > External Email - Use Caution > Dear Freesurfer experts, > > I'm trying to run a simulation (--> mri_glmfit-sim) with cached LGI > data (fwhm10), but get an error due to the estimated fwhm kernel. > The folder corresponding to the fwhm value (-->37) does not exist, I > guess because it's a pretty unusual value...? > > DoSim = 0 > UseCache = 1 > DoPoll = 0 > DoPBSubmit = 0 > DoBackground = 0 > DiagCluster = 0 > gd2mtx = dods > fwhm = 36.855100 > ERROR: cannot find > /apps/prod/x86_64/freesurfer-6.0.1/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/abs/th20/mc-z.csd I've seen mails describing similar issues in the archive and > from > your explanation I more or less understand that you cannot define > this value as it is estimated in the process...? However, I did not > see if there is a solution to this problem. What could I do about it > now? > > I attached the logfiles and would be very grateful for your help, > > thanks a lot and stay healthy, > > Doro > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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