then that is the "ocn" file to use with mri_segstats

On 02/21/2017 12:18 PM, Clara Kühn wrote:
> yes!
>
> ----- Ursprüngliche Mail -----
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 21. Februar 2017 17:58:37
> Betreff: Re: [Freesurfer] cluster as ROI
>
> Does this file exist?
>
> /nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
>
>
> On 02/21/2017 11:54 AM, Clara Kühn wrote:
>> I've attached it for you as a .txt file
>>
>> ----- Ursprüngliche Mail -----
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Dienstag, 21. Februar 2017 17:47:23
>> Betreff: Re: [Freesurfer] cluster as ROI
>>
>> Can you send the terminal output?
>>
>>
>> On 02/21/2017 11:44 AM, Clara Kühn wrote:
>>> Hm. I already did that. In none of my glmdirs are files like the 
>>> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
>>>
>>> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir 
>>> $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
>>>
>>> Cheers Clara
>>>
>>> ----- Ursprüngliche Mail -----
>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Dienstag, 21. Februar 2017 17:24:02
>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>
>>> You will have to run mri_glmfit-sim
>>>
>>>
>>> On 02/21/2017 04:07 AM, Clara Kühn wrote:
>>>> Hi Doug,
>>>>
>>>> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and 
>>>> I also have a contrasts.sig.mgh file in the gmldir.
>>>>
>>>> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could 
>>>> I retrieve this file?
>>>>
>>>> Thanks for your help!
>>>> Clara
>>>>
>>>> ----- Ursprüngliche Mail -----
>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Gesendet: Donnerstag, 16. Februar 2017 19:22:01
>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>
>>>> On 02/16/2017 04:24 AM, Clara Kühn wrote:
>>>>> Hi Doug,
>>>>>
>>>>> thanks for your input. Could you specify some of the flags for me?
>>>>>
>>>>> --i tp1.stack.mgh - is this supposed to be the cluster or file in my 
>>>>> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
>>>> input from preproc/surf2surf
>>>>> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this 
>>>>> file. The only files I have in the contrast folder are 2 .mat files
>>>> there should be a bunch of output there from mri_glmfit and
>>>> mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output
>>>> may not be there. you'll have to run it separately. But there should be,
>>>> eg, gamma.mgh there
>>>>> Cheers
>>>>> Clara
>>>>>
>>>>> ----- Ursprüngliche Mail -----
>>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>>> Gesendet: Mittwoch, 15. Februar 2017 23:35:54
>>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>>
>>>>> Use something like this
>>>>>
>>>>> mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
>>>>> --excludeid 0 --avgwf tp1.clustermean.dat
>>>>>
>>>>> The output tp1.clustermean.dat will be a matrix with nsubjects rows and
>>>>> nclusters columns where the value represents the mean for that subject
>>>>> in that cluster.
>>>>>
>>>>>
>>>>>
>>>>> On 02/14/2017 11:47 AM, Clara Kühn wrote:
>>>>>> Dear FreeSurfer Experts,
>>>>>>
>>>>>> I compared 2 groups in QDEC in spc (from pre to post) and found a 
>>>>>> cluster that survives Monte Carlo correction. Now I would like to 
>>>>>> extract the data for each participant and each time point from that 
>>>>>> cluster so that I can plot the change.
>>>>>>
>>>>>> How could I do this? I tried this so far:
>>>>>> aparcstats2table --qdec-long $SUBJECTS 
>>>>>> DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
>>>>>> $SUBJECTS 
>>>>>> DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt 
>>>>>> --parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
>>>>>> again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
>>>>>>
>>>>>> But I get this error:
>>>>>> ERROR: The stats file 
>>>>>> /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
>>>>>>  is not found or is too small to be a valid statsfile
>>>>>> Use --skip flag to automatically skip bad stats files
>>>>>>
>>>>>>
>>>>>> Do I have to define my cluster as a ROI and then warp it onto the single 
>>>>>> time points? How would I do that?
>>>>>>
>>>>>> Any help is much appreciated!
>>>>>> Thank you
>>>>>>
>>>>>> Clara
>>
>> _______________________________________________
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>> Freesurfer@nmr.mgh.harvard.edu
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-- 
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
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