Dear Doug,Thank you very much for your response. I am attaching my g3vo.txt
file -have changed extension now.I finally manage to make it work but I am not
confident if this is the ideal way of running a design for 3 groups 1 factor 3
levels no covariates as FS indicate
(https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V).
This is how I am running it:
mri_glmfit --glmdir rh.thickness.g3v0.glmdir --y rh.g3v0.thickness.15B.mgh
--fsgd g3v0.txt --C HC-BD_fam.mtx --C HC-BD.mtx --C BD-BD_fam.mtx --C
group.effect.mtx --C HC+BD-vs-BD_fam.mtx --surf fsaverage rh --cortex
And run separately for volume and white.But my question is should I be running
it using y.mgh instead (as below)? mri_glmfit \
--glmdir g3v0 \
--y y.mgh \
--fsgd g3v0.fsgd \
--C normal-mci.mtx \
--C normal-ad.mtx \
--C mci-ad.mtx \
--C group.effect.mtx \
--C normal+mci-vs-ad.mtxBut my problem is that I would need to run in Qdec
and this is not for more than 2 group analyses?Many thanks!Pablo
> Date: Wed, 8 Jul 2015 17:35:21 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] 3 Group comparison
>
> There is not a --meas option for mri_glmfit, you need to give it a --y
> option explicity, though it may be trying to read a yfile if you have
> one in the FSGD. How did you make g3v0.fsgd? Can you send it? The second
> command looks like you are doing the right thing, you just need to tell
> mri_glmfit that this is surface data by adding --surface fsaverage hemi
>
> where hemi is lh or rh
>
> doug
>
> On 07/07/2015 06:45 AM, pablo najt wrote:
> > Dear FS experts,
> > I am trying to run a 3 group comparison with FS.
> > I have run preproc ( script from ENIGMA Cortical protocol) on my first
> > fsgd file.
> >
> > As I have three groups I have prepared my second fsgd file as g3v0.fsgd
> > and all my desired contrasts, rather than using QDEC.
> >
> > I run this second stage as follows:
> > mri_glmfit \
> > --glmdir g3v0 \
> > --meas thickness ../SURF/lh.thickness.mgh \
> > --fsgd g3v0.fsgd \
> > --C HC-BD_fam.mtx \
> > --C HC-BD.mtx \
> > --C BD-BD_fam.mtx \
> > --C group.effect.mtx \
> > --C HC+BD-vs-BD_fam.mtx
> >
> > and I get:
> >
> > Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh
> >
> > mghRead(/Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh, -1): could
> > not open file
> >
> > ERROR: loading y /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh
> >
> >
> > As far as I understand y.mgh is a stack data that is made after using
> > QDEC is run. But I have been prompted to not use QDEC, so I am now
> > wondering how I am supposed to run my glm design.
> >
> > Also I tried to change the y.mgh to any of the outputs of the
> > mris_preproc (lh.white.mgh, lh.volume.mgh, lh.thickness.mgh, etc), and
> > it says:
> >
> > Creating output directory g3v0
> >
> > Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/SURF/rh.white.mgh
> >
> > ERROR: you must use '--surface subject hemi' with surface data
> >
> > Any suggestion would be greatly appreciated.
> > Thanks a lot.
> > Pablo
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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GroupDescriptorFile 1
Title OSGM
Class HC
Class BD
Class BD-Fam
Input 001ER BD
Input 011GB BD
Input 018AM HC
Input 045PC BD-Fam
Input 054JB HC
Input 058CS BD
Input 062AH BD-Fam
Input 093DC HC
Input 095RA HC
Input 103FC_6 BD
Input 108JMCM HC
Input 117AS HC
Input 121JB BD
Input 137ED BD
Input 156PMC HC
Input 176VOD HC
Input 192AL HC
Input 204PC BD-Fam
Input 214VH BD-Fam
Input 229PK HC
Input 240PE HC
Input 285SK HC
Input 300VW BD-Fam
Input 301EK HC
Input 338JM HC
Input 352DFc BD
Input 383AW HC
Input 387SD BD
Input 389NM_first HC
Input 393AGG HC
Input 403SH BD-Fam
Input 409MCa BD-Fam
Input 414MOB HC
Input 421JC HC
Input 427LH HC
Input 433MON HC
Input 456MWb BD
Input 492HGc BD-Fam
Input 501POT HC
Input 512EQ HC
Input 569AG HC
Input 574BH HC
Input 578DCa BD
Input 582RG HC
Input 585AOD BD
Input 589JL BD-Fam
Input 596JT HC
Input 620CB BD-Fam
Input 635AG HC
Input 655PMCE HC
Input 660AQ HC
Input 668JG BD-Fam
Input 673JK HC
Input 703MHc BD
Input 718PJ BD
Input 741JT HC
Input 750MD BD-Fam
Input 777MCb BD
Input 783DMCM HC
Input 792GF BD
Input 807YG HC
Input 818NL HC
Input 853MR HC
Input 868ALF BD-Fam
Input 888MOB HC
Input 896EF BD
Input 914JB HC
Input 917JH HC
Input 923BOM BD-Fam
Input 930TL BD
Input 948SC HC
Input 984PL HC
Input 989OB HC
Input 997SG HC
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The information in this e-mail is intended only for the person to whom it is
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