Re: [Freesurfer] Qdec 1.5

if that file does not exist, then it will crash. That file should be created by recon-all. Is that file not there?

On 04/28/2017 05:22 AM, Duy Nguyen wrote:

Hello Douglas

Thank you for your response. I have just run the subjects from the data on OASIS through qdec and I followed the steps on freesurfer.

Everything is ok until the step of pressing 'Generate Stats Data Tables' that I have asked you before somehow I keep getting the same issue. There is the following error log being attached to this email. From the log, it was asking me for the wmparc.stats, but somehow my subjects'stats directory does not have that file. How can I change to lh.aparc.stats but I want to analyze the cortical thickness.

Your help is appreciated.

Thank you and best regards

*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*

On Fri, Mar 24, 2017 at 10:11 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

does that file exist? If it does, look at its contents and compare
it to
others in terms of size


On 3/24/17 9:11 AM, Duy Nguyen wrote:
> Dear Doughlas
>
> When I tried to run the aparcstats2table command, it shows the
following
> error in the terminal window:
> SUBJECTS_DIR : /home/toibigi2007/Desktop
> Parsing the .stats files
> ERROR: The stats file
> /home/toibigi2007/Desktop/004/stats/lh.aparc.stats is not found
or is
> too small to be a valid statsfile
> Use --skip flag to automatically skip bad stats files
>
> The group of subjects is from the tutorial data set.
> Please help me sort this out.
>
> Thank you and best regards,
>
>
> *--v-- Peace --v--*
> *Duy Nguyễn *
> *Biomedical Engineering Department- IU HCMC*
> *Cell: (+84)909999056*
> *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>
<duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>>*
>
> On Thu, Mar 23, 2017 at 10:23 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>> wrote:
>> need more info
>>
>>
>> On 03/22/2017 09:37 PM, Duy Nguyen wrote:
>>> Dear Douglas
>>>
>>> Thank you for your response.  I cannot run asegstats2table and
>>> aparcstats2table command outside of qdec.
>>>
>>> Best regards,
>>> Duy Nguyen
>>>
>>> *--v-- Peace --v--*
>>> *Duy Nguyễn *
>>> *Biomedical Engineering Department- IU HCMC*
>>> *Cell: (+84)909999056*
>>> *Email: duy.nguyenbme@gmail.com
<mailto:duy.nguyenbme@gmail.com> <mailto:duy.nguyenbme@gmail.com
<mailto:duy.nguyenbme@gmail.com>>*
>>>
>>> On Thu, Mar 23, 2017 at 5:07 AM, 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:
>>>
>>>      don't know what is going on there. Can you run the
asegstats2table
>>>      command outside of qdec?
>>>
>>>
>>>      On 3/17/17 8:29 AM, Duy Nguyen wrote:
>>>>      Dear FS Expert
>>>>
>>>>      I am doing analysis from the group_analysis_tutorial data to
>>>>      practice and learn.  However, I come across the error
window like
>>>>      it shows on the attached picture (please see the
attachment) when
>>>>      I press the button "Generate Stats Data Table." Please
help me
>>>>      how can I can find the file aseg.volume.stats.dat. If
the file
>>>>      does not exist, how can I create one?
>>>>
>>>>      Thank you for your response. Any help would be
appreciated!!!
>>>>      *--v-- Peace --v--*
>>>>      *Duy Nguyễn *
>>>>      *Biomedical Engineering Department- IU HCMC*
>>>>      *Cell: (+84)909999056*
>>>>      *Email: duy.nguyenbme@gmail.com
<mailto:duy.nguyenbme@gmail.com> <mailto:duy.nguyenbme@gmail.com
<mailto:duy.nguyenbme@gmail.com>>*
>>>>
>>>>
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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
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