Hi Jahanvi, 

1. yes, you need to create this table to then perform the stats

2. no, the format is as I described it below

fsid            fsid-base

tp1_subA  templatesubA

tp2_subA  templatesubA

tp1_subB  templatesubB

tp2_subB  templatesubB

this is assuming that you called your base templatesubA and templatesubB for the two subjects. It will automatically look in the

tp1_subA.long.templatesubA etc. directories. 

Best, Martin

On 12 May 2017, at 16:55, jahanvi patel <jahanvipatel.tw@gmail.com> wrote:

Hi Martin,

Do you mean by creating this long.testretest.qdec file, one can then perform the stats for the longitudinal2StageModel?

So for a 2 timepoints analysis, eg. TP1 & TP2.

 the long.testretest.qdec will be looking like this  ?

fsid                                             fsid-base

tp1_subA.long.TemplatesubA     tp2_subA.long.TemplatesubA

tp1_subB.long.TemplatesubB     tp2_subB.long.TemplatesubB

tp1_subC.long.TemplatesubC     tp2_subC.long.TemplatesubC

.

.

.

Thanks,

Jahanvi

tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh

Hi Jahanvi,

long.testretest.qdec is a qdec table in the longitudional format (with the fsid-base as the second column).

For test-retest (e.g. same session with subject removal), you usually don't need a time column, that is why --generic-time is specified. the qdec table would just look like

fsid fsid-base

me me_test

me me_retest

you you_test

you you_retest

...

Best, Martin

On 05/08/2017 04:10 PM, jahanvi patel wrote:

Hello list,

I have a simple question about the LongitudinalTwoStageModel tutorials on freesurfer website.

It is from this link

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

long_mris_slopes --qdec long.testretest.qdec \

      --meas thickness \

      --hemi lh \

      --sd $SUBJECTS_DIR \

      --do-pc1 --do-label \

      --generic-time \

      --fwhm 15 \

      --qcache fsaverage \

      --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \

      --isec-labels lh.testretest.fsaverage.cortex.label

My question is, what is the content of  long.testretest.qdec ?

I understood till 1st stage was done, we got only one file which is long.qdec.table.dat.

Could anyone help to clarify my question?

Thanks a lot

Jahanvi

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