Hi Doug,

The very first command line was:

mri_glmfit-sim \

  --glmdir /Volumes/RainvilleHD2/Imaging_Data/Thickness/MATHIEUP_IBS/FS_1stAnalysis/GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \

  --sim mc-z 5000 3 mc-z.abs.3 \

  --cwpvalthresh .05 \

  --sim-sign abs \

  --overwrite

I was wondering, since the purpose of running mri_glmfit-sim at  --cwpvalthresh .999 is to see all clusters, would it be the same if I were simply to look at sig.mgh?

Thanks.

Jeni

Sorry, I mean the first time that you ran it to create the csd files in 
the first place
doug

On 2013-04-25, at 5:30 PM, Jeni Chen wrote:

The original command line:

> mri_glmfit-sim \
> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \
> --cwpvalthresh .999 \
> --no-sim GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd

To which you suggested

> mri_glmfit-sim \
> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \
> --cwpvalthresh .999 \
> --no-sim 1GroupAvg-Cor-thickness-Mod-VAS

And it did not work either.

Thanks.

jeni

Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700

> what was your orignal mri_glmfit-sim command line?

On 04/25/2013 05:17 PM, Jeni Chen wrote:
> Hi Doug,
>
> Sorry; didn't realize it wasn't included.
>
> So to state the original problem, I tried running mri_glmfit-sim with 
> the following options (previous message included below):
>
> mri_glmfit-sim \
> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \
> --cwpvalthresh .999 \
> --no-sim 
> GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd
>
> I get an error message saying "cannot find any csd files". You 
> suggested putting just the csd base 
> (i.e. 1GroupAvg-Cor-thickness-Mod-VAS) for the --no-sim flag, which I 
> did, but still gave the same error message. I've attached the error 
> log if you want to have a look.
>
> Thanks.
>
> Jeni
>
>
>
>
>> Hi Jeni, what is your command line and terminal output? In general, 
>> just saying that something does not work is not enough information to 
>> track down the problem. Also, please include previous correspondence. 
>> We answer a lot of emails here, and the easier you make it on us, the 
>> faster we can solve your problem. thanks! doug
> On 04/25/2013 04:41 PM, Jeni Chen wrote:
> > Thansk Doug. I tried it but still doesn't work. Any other thoughts?
> >
> > jeni
> >
> >
> > _______________________________________________
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> >Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
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> >
>> Hi Jeni, done pass that path to the csd, just the csd base. In your 
>> case I think it would be 1GroupAvg-Cor-thickness-Mod-VAS
>> doug
>>> On 4/24/13 8:47 PM, Jeni Chen wrote:
>>
>>     Hello,
>>
>>     I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I
>>     specified the --no-sim option to avoid re-running the entire
>>     simulation again. I entered my DSC file but in the end I get the
>>     error message: "cannot find any csd files". Here is what I entered:
>>
>>     mri_glmfit-sim \
>>     --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \
>>     --cwpvalthresh .999 \
>>
>>     --no-sim
>>     
>> GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csdI
>>     copied and pasted the csd file from its own folder to the top
>>     directory, but it gave the same error. I've attached the error
>>     log in case you want to have a look.
>>
>>     Thanks for your help!
>>
>>     Jeni
>>
>
>
>
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