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