On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve <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>> 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> 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>
>> *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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--
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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