Re: [Freesurfer] Longitudinal Analysis Error

Hi Silvia,

it is never a good idea to mix versions and we did not test any such combinations. Also because 5.1 is much better than 4.5 I would definitely recommend to rerun.

However, I still believe that it should be possible to use the 5.1 post-processing scripts to e.g. create rate maps for each subject and qdec to analyze them even with 4.5 processed data.

Best, Martin

On Tue, 2011-07-26 at 10:45 +0200, Silvia Juanes wrote:

Hi Martin,

We used the preprocessing pipeline from 4.5 version and then we used the 5.1 version to perform the longitudinal analysis. Do you think that we should repeat the preprocessing using 5.1 version? or do you know any other solution to do the analysis with the 4.5 preprocessing data?

Best,

Silvia

2011/7/25 Martin Reuter mreuter@nmr.mgh.harvard.edu Hi Silvia,

    qdec does not support any longitudinal analysis (only cross
    sectional).
    So I assume you either compare groups cross sectionally (e.g.
    at
    baseline) or you constructed your own longitudinal measure
    (e.g. percent
    change, within each subject) and then do a cross sectional
    analysis of
    that statistic?
    Both these things should work. I think your qdec table is
    setup
    incorrectly?

    Best, Martin


    On Tue, 2011-07-19 at 12:45 +0200, Silvia Juanes wrote:
    > Dear all,
    > We are preprocessed our data to perform a longitudinal study
    using
    > longitudinal pipeline of Freesurfer 4.5. However, when we
    try to do
    > the group-analysis using qdec (Freesurfer 5.1), we obtain
    the
    > following error:
    >
    >
    > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have
    2 levels
    > ninputs = 64
    > Checking inputs
    > nframestot = 64
    > Allocing output
    > Done allocing
    > nframes = 64
    > Writing to /home/barbara/subjects/qdec/Untitled/y.mgh
    > gdfReadHeader:
    reading /home/barbara/subjects/qdec/Untitled/qdec.fsgd
    > INFO: gd2mtx_method is dods
    > Reading source
    surface /home/barbara/subjects/fsaverage/surf/lh.white
    > ERROR: no contrasts specified.
    > Error in Analyze: command failed: mri_glmfit
    > --y /home/barbara/subjects/qdec/Untitled/y.mgh
    > --fsgd /home/barbara/subjects/qdec/Untitled/qdec.fsgd dods
    > --glmdir /home/barbara/subjects/qdec/Untitled --surf
    fsaverage lh
    >
    >
    >
    > Has anyone experienced a similar problem and is there any
    way to correct it?
    >
    >
    > Best,
    >
    >
    >

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