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is there a way to visualize the changes in thickness, area, and volume between
the 2 timepoints (cortical and subcortical)? I was under the impression that
running mri_preproc would aloow me to visualize change in cortical thickness bt
the 2 timepoints (lh.paired.thickness.mgh).
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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Friday, May 1, 2020 12:14 PM, Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:
> Oh, right. You only have one data point (the difference) and you are
> computing one parameter (the mean), so you have 0 DOF. If you only have one
> data point, there are not statistical tests you can do
>
> On 5/1/2020 3:34 AM, KennethSPrice wrote:
>
>> External Email - Use Caution
>>
>> In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and
>> it is the only group. However, I removed --fsgd and replaced it with --osgm
>> upon your reccomendation, and am still getting the error.
>>
>> I am also having an issue visualizing the output of mri_preproc in freeview
>> - isnt this mgh file supposed to be a volume? Is there a way to center the
>> freeview cursor to the middle of the current volume?
>>
>> Thanks,
>> Ken
>>
>> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
>> On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve
>> <dgr...@mgh.harvard.edu> wrote:
>>
>>> how many subjects are there in your fsgd? How many groups in your fsgd
>>> file? Also, you should not use --osgm and --fsgd
>>>
>>> On 4/30/2020 1:09 PM, KennethSPrice wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Hello Freesurfer friends!
>>>>
>>>> I'm going through the "paired analysis" tutorial and am running into an
>>>> issue with the mri_glmfit. I am running on just one subject pair.
>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
>>>>
>>>> I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit
>>>>
>>>> mris_preproc --target fsaverage --hemi lh \
>>>> --meas thickness --out lh.paired-diff.thickness.mgh \
>>>> --fsgd pairs.fsgd --paired-diff
>>>>
>>>> mri_glmfit \
>>>> --glmdir lh.paired-diff \
>>>> --y lh.paired-diff.thickness.sm05.mgh \
>>>> --fsgd paired-diff.fsgd \
>>>>
>>>> --osgm \
>>>>
>>>> --surf fsaverage lh
>>>>
>>>> I am getting an ERROR: DOF = 0.
>>>>
>>>> MRI's have been put through recon-all and are in there own directories
>>>> within SUBJECTS_DIR.
>>>>
>>>> What is the cause of the error?
>>>>
>>>> Thanks,
>>>>
>>>> Ken
>>>>
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