Re: [Freesurfer] mri_glmfit error with aparc table flag

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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--
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MGH-NMR Center
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