On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Sorry, I don't have another solution for you.

On 04/19/2017 01:42 PM, miracle ozzoude wrote:
> Thanks Doug. However, I am running freesurfer analysis on my personal
> computer and I don't have matlab. Also, I don't know how this matlab
> script works/ matlab works. Any instructions on how to use it or
> alternate? Please and thank you.
> Best,
> Paul.
>
> On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> It is a table of data, so you can't visualize it directly on anything.
> You can try using annotval2surfoverlay.m to create a surface
> overlay of
> the data.
>
>
> On 04/19/2017 10:05 AM, miracle ozzoude wrote:
> > Hello Doug,
> > It worked. The issue was due to formatting error with the aparc
> file.
> > Also, I was trying to visualize the result on the surface using
> > freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on
> > freeview and loading the sig.mgh). However, i got an error "
> failed to
> > display overlay". How can I visualize the result? Thanks
> > Best,
> > Paul
> >
> > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > You have a table of data, so no template is needed. If you
> put the
> > --surf before the --table, it probably runs, but it will ignore
> > the surface
> >
> >
> > On 4/18/17 9:58 PM, miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> wrote:
> >> Thanks doug. Does it mean when using the --table flag, you
> can't
> >> use the fsaverage template? I came across several post in the
> >> forum that used "--surf fsaverage lh "‎ and it worked.
> >> Best,
> >> Paul
> >>
> >> Sent from my BlackBerry 10 smartphone.
> >> *From: *Douglas Greve
> >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> >> *To: *freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >> <mailto:freesurfer@nmr.mgh.harvard.edu

> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> >> *Reply To: *Freesurfer support list
> >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc
> table flag
> >>
> >>
> >> Don't include --surf fsaverage lh. It thinks the input is a
> >> surface, not a table
> >>
> >>
> >>
> >> On 4/18/17 9:21 PM, miracle ozzoude wrote:
> >>> Hello freesurfer,
> >>> I am trying to run mri_glmfit with the --table flag. My
> >>> aparc_lh_thick_stats.txt contain entorhinal and
> parahippocampal
> >>> thickness values for 32 subjects. I ran the glm command and
> >>> received an error. Please, how can i solve this issue? I have
> >>> included my command, fsgd file, contrast matrix and error
> below.
> >>> Thanks
> >>> Best,
> >>> Paul
> >>>
> >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt
> --fsgd
> >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh
> --cortex
> >>> --glmdir lh.thickness.glmdir
> >>>
> >>>
> >>> ERROR= "gdfRead(): reading age.fsgd
> >>>
> >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be
> done.
> >>>
> >>> Continuous Variable Means (all subjects)
> >>>
> >>> 0 Age 39.9375 17.3312
> >>>
> >>> Class Means of each Continuous Variable
> >>>
> >>> 1 Group1 35.6316
> >>>
> >>> 2 Group2 46.2308
> >>>
> >>> INFO: gd2mtx_method is dods
> >>>
> >>> Reading source surface
> >>>
> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
> >>>
> >>> Number of vertices 163842
> >>>
> >>> Number of faces 327680
> >>>
> >>> Total area 65416.984375
> >>>
> >>> AvgVtxArea 0.399269
> >>>
> >>> AvgVtxDist 0.721953
> >>>
> >>> StdVtxDist 0.195470
> >>>
> >>>
> >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman
> Exp $
> >>>
> >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri
> >>>
> >>> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd
> >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh
> --cortex
> >>> --glmdir lh.thickness.glmdir
> >>>
> >>> sysname Darwin
> >>>
> >>> hostname MacBook-Pro.local
> >>>
> >>> machine x86_64
> >>>
> >>> user MiracleOz
> >>>
> >>> FixVertexAreaFlag = 1
> >>>
> >>> UseMaskWithSmoothing 1
> >>>
> >>> OneSampleGroupMean 0
> >>>
> >>> y
> >>>
> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> >>>
> >>> logyflag 0
> >>>
> >>> usedti 0
> >>>
> >>> FSGD age.fsgd
> >>>
> >>> labelmask
> >>>
> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
> >>>
> >>> maskinv 0
> >>>
> >>> glmdir lh.thickness.glmdir
> >>>
> >>> IllCondOK 0
> >>>
> >>> ReScaleX 1
> >>>
> >>> DoFFx 0
> >>>
> >>> Creating output directory lh.thickness.glmdir
> >>>
> >>> Loading y from
> >>>
> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> >>>
> >>> Found 66 data colums
> >>>
> >>> Found 0 data rows
> >>>
> >>> INFO: gd2mtx_method is dods
> >>>
> >>> Saving design matrix to lh.thickness.glmdir/Xg.dat
> >>>
> >>> Computing normalized matrix
> >>>
> >>> Normalized matrix condition is 32.2165
> >>>
> >>> Matrix condition is 20734.7
> >>>
> >>> Found 149955 points in label.
> >>>
> >>> ERROR: mri_reshape: number of elements cannot change
> >>>
> >>> nv1 = 163842, nv1 = 66
> >>>
> >>> search space = 82219.962936
> >>>
> >>> ERROR: dimension mismatch between y and X.
> >>>
> >>> y has 0 inputs, X has 32 rows."
> >>>
> >>> FSGD file: GroupDescriptorFile 1
> >>>
> >>> Title MOT
> >>>
> >>> Class Group1
> >>>
> >>> Class Group2
> >>>
> >>> Variables Age
> >>>
> >>> Input 01053p Group1 23
> >>>
> >>> Input 01054p Group1 43
> >>>
> >>> Input 01061p Group2 39
> >>>
> >>> Input 01062p Group2 19
> >>>
> >>> Input 01074p Group2 28
> >>>
> >>> .............. (I have more participants)
> >>>
> >>>
> >>> CONTRAST MATRIX: 1 -1 0 0
> >>>
> >>>
> >>>
> >>> _______________________________________________
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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