[Freesurfer] Monte Carlo for lme

External Email - Use Caution Dear Freesurfer experts, I am looking into Monte Carlo simulation to control for multiple comparisons for lme in Matlab. Are there any good library that has implemented this in Matlab? Best regards Knut Jørgen Bjuland PhD

Re: [Freesurfer] Monte Carlo threshold p-values

1.3 is not a z value, it is -log10(.05) On 07/06/2018 10:15 AM, Dincer, Aylin wrote: > > > Hello FreeSurfer experts, > > > In the FreeSurfer wiki page regarding multiple comparisons > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons > ) under "Simulation", it

Re: [Freesurfer] Monte Carlo simulation - vertex wise threshold question

Yes, 3 is p<.001, which is converted to a z before thresholding the map. Note that we are trying to push people to use permutation instead of MC. On 07/09/2018 05:22 PM, Dincer, Aylin wrote: > > > Hi FreeSurfer experts, > > > I am trying to understand the Monte Carlo Z simulation in FreeSufer >

[Freesurfer] Monte Carlo simulation - vertex wise threshold question

External Email - Use Caution Hi FreeSurfer experts, I am trying to understand the Monte Carlo Z simulation in FreeSufer (mri_glmfit-sim) and have a question about the vertex wise /cluster forming threshold. In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set

[Freesurfer] Monte Carlo threshold p-values

External Email - Use Caution Hello FreeSurfer experts, In the FreeSurfer wiki page regarding multiple comparisons (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons ) under

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

I don't know, you'll have to look at how you computed the first frame. Maybe the 1st and 2nd time point for that subject are the same On 02/05/2018 04:27 PM, miracle ozzoude wrote: > Hello Doug, > > Thank you. How do i got about fixing? Do you think it's a good idea to > start afresh on this

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Hello Doug, Thank you. How do i got about fixing? Do you think it's a good idea to start afresh on this subject (i.e. recon-all and longitudinal pipeline)? Best, Paul On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve wrote: > The first frame in your input file is all

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

The first frame in your input file is all 0s, so something is wrong with the fist subject On 2/3/18 3:03 PM, miracle ozzoude wrote: Hello Doug, I have uploaded the files you requested. Thank you for your help. Best, Paul On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Hello Doug, I have uploaded the files you requested. Thank you for your help. Best, Paul On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve wrote: > Can you upload the glmfit folders and the glmfit input (--y file) to our > filedrop? > >

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Can you upload the glmfit folders and the glmfit input (--y file) to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ On 2/1/18 7:46 PM, miracle ozzoude wrote: Hello Doug, I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask On 1/20/18 1:56 PM, miracle ozzoude wrote: Hello Doug, I tried using the MC tables that FS distributed. However, i got an error about " cannot find

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Hello Doug, I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Hello Doug, Thanks for responding. I am running a whole brain analysis as result shouldn’t I build my own MC simulation? Best, Paul Sent from my iPhone > On Jan 18, 2018, at 5:23 PM, Douglas Greve wrote: > > Why are you doing your own MC simulation? You can just

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Why are you doing your own MC simulation? You can just use the tables that we distribute ... On 1/17/18 6:12 PM, miracle ozzoude wrote: Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page

[Freesurfer] monte-carlo error in longitudinal pipeline

Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page ( https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd

Re: [Freesurfer] Monte-Carlo f-test

In theory it is because the F can be converted to a p which can be converted into a pseudo-z. When you run mri_glmfit-sim, you should make sure to use an unsigned test ("abs") On 12/22/17 8:08 PM, basile pinsard wrote: Hi Freesurfer experts. Does mri_glmfit-sim Monte-Carlo cluster size

Re: [Freesurfer] Monte-Carlo correction and 3-groups comparison

It is appropriate. The F-test is not the same as t-test, so it is not totally surpising that you get different results On 12/22/17 5:06 PM, Pauline Duret wrote: Hello all, I am running a gyrification analysis between 3 groups. So I modeled my GLM like the one on this page:

[Freesurfer] Monte-Carlo f-test

Hi Freesurfer experts. Does mri_glmfit-sim Monte-Carlo cluster size correction is also usable for F-test? The doc says that it synthesizes a z map (I assume from a normal distribution) for computing the voxel-wise thresholds and cluster size distribution. Maybe I am wrong with my stats but I

[Freesurfer] Monte-Carlo correction and 3-groups comparison

Hello all, I am running a gyrification analysis between 3 groups. So I modeled my GLM like the one on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V I was wondering if it is correct to run a Monte-Carlo correction on the

Re: [Freesurfer] Monte-Carlo in LME

yes On 7/21/17 5:24 AM, Jordi Pegueroles wrote: > Thank you Doug. So, instead of running mri_surfcluster I should run > mri_glmfit-sim with the --fwhm-override with the smoothing obtained > from the residuals of the lme model. > > Thanks again, > > A 2017-07-18 22:09, Douglas N Greve escrigué:

Re: [Freesurfer] Monte-Carlo in LME

Thank you Doug. So, instead of running mri_surfcluster I should run mri_glmfit-sim with the --fwhm-override with the smoothing obtained from the residuals of the lme model. Thanks again, A 2017-07-18 22:09, Douglas N Greve escrigué: > Not sure. It might be more accurate. Once you have the FWHM

Re: [Freesurfer] Monte-Carlo in LME

Not sure. It might be more accurate. Once you have the FWHM you want, you can run mri_glmfit-sim with --fwhm-override On 07/17/2017 05:43 PM, Jordi Pegueroles wrote: > Dear FS experts, > > I was wondering if someone had performed multiple comparisons (ie > monte-carlo) with the LME analyses. I

[Freesurfer] Monte-Carlo in LME

Dear FS experts, I was wondering if someone had performed multiple comparisons (ie monte-carlo) with the LME analyses. I have found a thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) where Doug recommends to run a GLM fit with the same data and then overwrite

Re: [Freesurfer] Monte Carlo error (fwhm4 vs. fwhm04)

Hi Eli, I would advise against trying to run MC inside of QDEC. Use mri_glmfit-sim instead On 06/01/2017 04:33 PM, Rockers, Elijah D. wrote: > Hello FS, > > I am attempting to run a monte carlo simulation on some cortical > thickness data in Qdec 1.5, but I get the following error: > > ERROR:

[Freesurfer] Monte Carlo error (fwhm4 vs. fwhm04)

Hello FS, I am attempting to run a monte carlo simulation on some cortical thickness data in Qdec 1.5, but I get the following error: ERROR: CSDread(): could not open ../freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th40/mc-z.csd I thought it might be a permissions issue

Re: [Freesurfer] monte carlo continue/ desktop restarted

Thank you On Wed, Sep 28, 2016 at 3:49 PM, Douglas Greve wrote: > There is no way. Yes, you can specify fsaverage for yoursubject > > On 9/28/16 3:47 PM, miracle ozzoude wrote: > > Hello Doug, > Do you know if there's any command to make it continue from where it >

Re: [Freesurfer] monte carlo continue/ desktop restarted

There is no way. Yes, you can specify fsaverage for yoursubject On 9/28/16 3:47 PM, miracle ozzoude wrote: Hello Doug, Do you know if there's any command to make it continue from where it stopped in case of future incidents? Also, what does " yoursubject" mean in this code? Can I substitute

Re: [Freesurfer] monte carlo continue/ desktop restarted

Hello Doug, Do you know if there's any command to make it continue from where it stopped in case of future incidents? Also, what does " yoursubject" mean in this code? Can I substitute it with fsaverage? Thanks Paul mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/rh/cortex \

Re: [Freesurfer] monte carlo continue/ desktop restarted

Thank you Doug Paul On Wed, Sep 28, 2016 at 10:39 AM, Douglas N Greve wrote: > I would just use what was created. There is nothing magical about 10,000 > iterations. A few iterations short won't make any difference. > > > On 09/28/2016 10:35 AM, miracle ozzoude

Re: [Freesurfer] monte carlo continue/ desktop restarted

I would just use what was created. There is nothing magical about 10,000 iterations. A few iterations short won't make any difference. On 09/28/2016 10:35 AM, miracle ozzoude wrote: > Hello experts, > I was running 1 monte carlo simulation before my desktop > automatically restarted, does

[Freesurfer] monte carlo continue/ desktop restarted

Hello experts, I was running 1 monte carlo simulation before my desktop automatically restarted, does anyone know a command to continue from where it stopped? The simulation for left hemisphere stopped at 9146/1 and right hemisphere at 9125/1. Thank you Paul

[Freesurfer] Monte Carlo correction in QDEC

Dear FreeSurfer experts, for the analysis in QDEC I created my own Monte Carlo correction. My questions relate to the threshold option. 1. Would I use neg if I have mostly blue clusters in the QDEC display and pos if I have mostly red clusters? 2. When do I use abs? 3. I compared the neg

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

Hi DOug, doug.log is attached the bash equivalent for |& is 2>&1 | thanks, Susan On Tue, 3 Nov 2015, Douglas N Greve wrote: I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

Can you run mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log and send me doug.log? On 11/02/2015 05:08 PM, s...@u.washington.edu wrote: > Hi experts, > > I am having trouble performing a

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in On 11/03/2015 01:41 PM, s...@u.washington.edu wrote: > Hi Doug, > > Do you mean: > >mri_glmfit-sim --debug --glmdir >

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

it cannot find this file /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat which should have been created by mri_glmfit. What is your mri_glmfit command line? Also, don't use --grf, that is for volumes only On 11/03/2015 02:27 PM,

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

Hi Doug, Do you mean: mri_glmfit-sim --debug --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log? When I tried running the same code with |& tee doug.log at the end, I kept

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

I am using bash. I am trying to google the bash equivalent of tcsh |&, but if anybody knows it, please let me know. thanks, Susan On Tue, 3 Nov 2015, Douglas N Greve wrote: > I meant &. The & works for tcsh (or csh). Are you using bash? I'm not > sure what the bash equivalent is. Maybe |2

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

Thanks. But it is still unsuccessfully looking for "rh.cope7.mgh" in [mydata}/cope7ACroi_rh.osgm.rfx. There are a lot of .mgh files in there (ar1, beta, mask, rstd, rvar, sar1), and even more .mgh files in cope7ACroi_rh.osgm.rfx/osgm (cnr, F, gamma, gammavar, mask, and sig) but no

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

The correct command line is --cache 4 neg --cache-label AC On 11/03/2015 03:36 PM, s...@u.washington.edu wrote: > Hi Doug, > > > > So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot > find any documentation about what to put instead of --grf), as in > > mri_glmfit-sim --glmdir

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

The fwhm.dat file was in the right place. You passed the wrong folder to mri_glmfit-sim. You should pass it cope7ACroi_rh.osgm.rfx doug On 11/03/2015 02:40 PM, s...@u.washington.edu wrote: > It's: > > mri_glmfit --y > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh >

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

It's: mri_glmfit --y /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh --osgm --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx --surf fsaverage lh --label /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label fwhm.dat

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

When you ran mri_glmfit the first time, you had to specify a file with the --y flag. It is looking for that file now. Does that file still exist in the location where it was when you ran mri_glmfit? On 11/03/2015 04:50 PM, s...@u.washington.edu wrote: > Thanks. But it is still unsuccessfully

[Freesurfer] Monte Carlo in mri_glmfit-sim

Hi experts, I am having trouble performing a Monte Carlo correction using mri_glmfit-sim. My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data. I want to do my analysis/correction only in auditory cortex (AC) so I did my own

Re: [Freesurfer] Monte Carlo correction

No, QDEC is a very limited tool. You'll have to use the command line (mri_glmfit-sim). Also, you'll need to register each of your subjects to the new atlas (surfreg), then specify the average subject AND the new registration when running mris_preproc to create a new y.mgh file. None of this

[Freesurfer] Monte Carlo correction

Dear all, During my analysis for pial_lgi instead of using fsaverage I prepared my own average surface using make_average and recon-all qcache. Now, I want to correct the results for multiple comparisons using Monte Carlo Null-Z simulation in Qdec. However, when I use my own average as

Re: [Freesurfer] Monte Carlo Simulation

...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 12, 2015 10:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Yes, that probably is the reason. doug On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote

Re: [Freesurfer] Monte Carlo Simulation

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Yes, that probably is the reason. doug On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote: To be honest, I checked the between subject alignment and it looked pretty good. None of my subjects was way out of alignment. However

Re: [Freesurfer] Monte Carlo Simulation

...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, March 11, 2015 3:22 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Something went very wrong with your first level

Re: [Freesurfer] Monte Carlo Simulation

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 12, 2015 2:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I meant which ones are causing the problems when you run mri_glmfit. When

Re: [Freesurfer] Monte Carlo Simulation

Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, March 11, 2015 6:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation For the range, lower is better, but it impossible to say exactly what is good enough because it depends on your data. If it is 0.8

Re: [Freesurfer] Monte Carlo Simulation

[gr...@nmr.mgh.harvard.edu] Sent: Wednesday, March 11, 2015 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Try checking the individual registrations (or look at the first value in the .mincost file) to find subjects whose registration may have been

Re: [Freesurfer] Monte Carlo Simulation

: Thursday, March 12, 2015 2:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I meant which ones are causing the problems when you run mri_glmfit. When you run fslview you will see something that looks like a brain. As you scroll thru the different time points

Re: [Freesurfer] Monte Carlo Simulation

? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 12, 2015 12:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation

Re: [Freesurfer] Monte Carlo Simulation

Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 12, 2015 12:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation If the registration looks ok, then that is all that counts. However, I'm a bit sceptical that the reg looks ok but the mincost is that much

Re: [Freesurfer] Monte Carlo Simulation

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, March 11, 2015 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I still can't really tell what it is doing. It looks like it is just

Re: [Freesurfer] Monte Carlo Simulation

. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, March 11, 2015 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I still can't

Re: [Freesurfer] Monte Carlo Simulation

: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, March 11, 2015 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I still can't really tell what

Re: [Freesurfer] Monte Carlo Simulation

, 2015 3:22 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Something went very wrong with your first level analysis because the final mask is pretty messed up. how did you create cbf.talairach.mgz ? On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote

Re: [Freesurfer] Monte Carlo Simulation

, 2015 3:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Sorry, I don't have time to deconstruct that script. Can you simplify it for me? On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote: This is the script I am using to create cbf.talaraich.mgz

Re: [Freesurfer] Monte Carlo Simulation

: [Freesurfer] Monte Carlo Simulation Sorry, I don't have time to deconstruct that script. Can you simplify it for me? On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote: This is the script I am using to create cbf.talaraich.mgz (attached). Thanks, Rick

Re: [Freesurfer] Monte Carlo Simulation

Hi Doug et al., Here is the glmdir file you were requesting: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928 Thanks, Rick From: Wolthusen, Rick Peter Fritz Sent: Tuesday, March 10, 2015 2:10 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: RE:

Re: [Freesurfer] Monte Carlo Simulation

Something went very wrong with your first level analysis because the final mask is pretty messed up. how did you create cbf.talairach.mgz ? On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug et al., Here is the glmdir file you were requesting:

Re: [Freesurfer] Monte Carlo Simulation

...@nmr.mgh.harvard.edu] Sent: Wednesday, March 11, 2015 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Try checking the individual registrations (or look at the first value in the .mincost file) to find subjects whose registration may have been off and so causes

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

mris_preproc might work. You could also use mri_concat (mris_preproc is a front end for mri_concat) On 03/03/2015 06:19 PM, Janosch Linkersdörfer wrote: Am 03.03.2015 um 14:42 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: Some of this Martin will have to comment on, but my comments

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

I don't know, esp since it is an approximation to begin with. An alternative is to take the offsets from your multi-time-point subjects and the single maps from your subjects with one time point and run that through the one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Am 03.03.2015 um 14:42 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: Some of this Martin will have to comment on, but my comments below On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote: Hey Doug, thanks again! That means, I would do something like: 1.) construct

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Some of this Martin will have to comment on, but my comments below On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote: Hey Doug, thanks again! That means, I would do something like: 1.) construct longitudinal qdec table - only use fsid, fsid-base, and years/age columns - substract the

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hey Doug, thanks again! That means, I would do something like: 1.) construct longitudinal qdec table - only use fsid, fsid-base, and years/age columns - substract the average age of the one-time point subjects from years/age value for every subject at every time point 2.) run long_mris_slopes

Re: [Freesurfer] Monte Carlo Simulation

Hi Rick, in the future please post to the list and not to us personally. Thanks! When you did the volume-based analysis, it should have masked out anything anything that was not subcortical. Did it not? If not, then when you run mri_glmfit you can add --mask

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hi Doug, thank you very much for your answer! Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: You would do the long analysis using a random effects analysis. OK, so basically do 2-stage modeling

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

You would do the long analysis using a random effects analysis. For each subject you can get a slope (this won't work if the subject only has 1 time point), then concatenate the slopes into a file and run mri_glmfit, then follow the procedures from the archive email you reference. doug On

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hi Doug and others, I would like apply (Monte Carlo simulation) cluster correction (as opposed to the implemented vertex-wise FDR correction) on the results from a longitudinal study I analyzed using the LME toolbox. The design is unbalanced (different number of time points, from 1 to 4, per

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, September 11, 2014 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh I think it must have gotten

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

, September 11, 2014 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh I think it must have gotten contaminated as an attachement. Try using this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim On 09/10

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

...@nmr.mgh.harvard.edu] Sent: Wednesday, September 10, 2014 4:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh Not sure what is wrong. Is it executable? Were you able to save the file from your email or did you cut and paste it into a file and save

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

: Thursday, September 11, 2014 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh I think it must have gotten contaminated as an attachement. Try using this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, September 09, 2014 6:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh Yes, you can just run /path/to/your/local/copy/mri_glmfit-sim On 09/09/2014 05:49 PM, Eryilmaz

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

09, 2014 6:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh Yes, you can just run /path/to/your/local/copy/mri_glmfit-sim On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote: Hi Doug, I don't seem to have the permission

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, September 10, 2014 4:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh Not sure what is wrong. Is it executable? Were you able to save the file

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, September 08, 2014 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh That was an oversight. I've

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh That was an oversight. I've attached a version that should work. Can you test it for me? Once I know it works I'll check it in to tree. doug On 09/03/2014 12:30 PM, Eryilmaz, Huseyin

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh You can just copy it over the old one (but make a backup of it first) On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote: Hi Doug, Thanks for your reply. I can certainly test it. Could you tell me how I can run this new

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, September 09, 2014 5:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh You can just copy it over the old one (but make a backup of it first) On 09/09/2014 04:21 PM

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

That was an oversight. I've attached a version that should work. Can you test it for me? Once I know it works I'll check it in to tree. doug On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote: Dear FS experts, I have a question about a MC output file. When I run the MC sim (using

[Freesurfer] Monte Carlo Sim output / sig.masked.mgh

Dear FS experts, I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However,

[Freesurfer] Monte Carlo correction

Hi there, I am trying to run a monte carlo correction on my average subject, using the full mri-mcsim run with 1 iterations (and about 200 participants). This is taking a long time, and the cluster I have access to has a limit of 72 hours which isn't long enough to finish processing. Is

[Freesurfer] Monte Carlo Cluster Size Threshold

Hello Freesurfer Experts, I am looking for the threshold cluster size used in a Monte Carlo Simulation (ran in qdec) at p=0.05. I believe the attached pdf (used to be mc-z.abs.th13.pdf) contains this information but I am not sure about how it is annotated. Does MaxClustBin correspond to a

Re: [Freesurfer] Monte Carlo Cluster Size Threshold

Just realized I didn't attach the pdf in the initial email. Sorry! On May 20, 2014, at 12:01 PM, Wegman, Clem J. wrote: Hello Freesurfer Experts, I am looking for the threshold cluster size used in a Monte Carlo Simulation (ran in qdec) at p=0.05. I believe the attached pdf (used to be

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Thanks, Doug! I looked at the examples on the wiki, and the Paired Analysis wiki page as well. You mentioned I should include the categorical and continuous variables in the fsgd file for the mri_glmfit. It seems that one of my analyses includes few subjects, and then one of the class end up

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

On 04/15/2014 10:34 PM, Pedro Rosa wrote: Hi, Doug. Thanks a lot! The command would look like this: mri_glmfit-sim --glmdir lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs --overwrite --cache 1.3 abs It takes only a few seconds to run. The command is fine, but remove --sim

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hi, Doug. Thanks a lot! The command would look like this: mri_glmfit-sim --glmdir lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs --overwrite --cache 1.3 abs It takes only a few seconds to run. I have a few questions about how to run it: 1) How the single entry for each subject

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Dear Doug and Jorge, I tried what you suggested and I think it work, although I have some concerns.I am working with a longitudinal study with two time-points for all subjects, three categorical variables (group, substance abuse / dependence

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

On 04/14/2014 10:35 AM, Pedro Rosa wrote: Dear Doug and Jorge, I tried what you suggested and I think it work, although I have some concerns. I am working with a longitudinal study with two time-points for all subjects, three categorical variables (group, substance abuse / dependence and

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Thanks, Doug! Should I run the mri_preproc and and smooth the output using mri_surf2surf with, let’s say, 10mm, and than run the LME normally in MatLab? Would this be problematic with a different smoothing procedure in mri_glmfit? How will mri_glmfit deal with the longitudinal design? Does this

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

I think I would just run mri_glmfit on your data to get the proper directly structure and estimate of FWHM, then copy the sig file from the mixed fx analysis into the glmfit folder for one of the contrasts. Then run mri_glmfit-sim. doug On 3/29/14 10:29 AM, Pedro Rosa wrote: Dear Doug

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Dear Doug and Jorge, Thank you very much for your help. I found another message in the list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) in which you suggested a way of using MC in mri_glmfit-sim by creating “fake files”, which would not be read by the

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Jorge, do you output the FWHM? doug On 03/27/2014 03:14 PM, jorge luis wrote: Hi Pedro Sorry, right now the only multiple comparisons corrections implemented in lme are the original Benjamini and Hochberg (1995) FDR procedure (lme_mass_FDR) and a more recent and powerful two-stage FDR

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hi Pedro Sorry, right now the only multiple comparisons corrections implemented in lme are the original Benjamini and Hochberg (1995) FDR procedure (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure (lme_mass_FDR2): Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006).

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Dear Doug, Thank you very much! I will try what you suggested, although I am not sure if Jorge's stream outputs the FMHM, or if I would need to run the statistics from the beggining using in the terminal, and not in MatLab. Do you think Jorge could comment on this issue? Regards, Pedro Rosa.

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