Hi Matthew, 

Thank you very much for all the explanation, I find it really helpful. I was wondering whether you could help me in understanding what the critical value is referring to after running the randomise command? I am for instance getting a critical value of 200256. 

Many thanks again,

Yvonne

On 30 May 2019, at 16:31, Matthew Webster <[log in to unmask]> wrote:

Hi Yvonne,

  This sounds that the output prefix for randomise was simply set to GM_mod_merg_s3. This is fine - the prefix can be set to whatever makes the results easy to identify.

Kind Regards

Matthew

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 30 May 2019, at 14:06, yvonne Van Hoecke <[log in to unmask]> wrote:

Hi Matthew, 

Thank you for getting back to me, I find it really helpful. Apologies if my questions seem straight forward, I am an FSL beginner! I tried to run my analysis again and everything seems to be running smoothly (the commands have not crashed and I am not getting any error messages). But for some reason I am not getting the fslvbm_tfce_corrp_tstat1 file in my stats subdirectory. I am however getting a GM_mod_merg_s3_tfce_corrp_tstat1.nii.gz. Would be grateful for any advice. 

Many thanks,

Yvonne

On 28 May 2019, at 14:17, Matthew Webster <[log in to unmask]> wrote:

Dear Yvonne,

1) The *JAC* files contain the Jacobian determinant for the registration ( described in more detail here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT/UserGuide#A--jout )

2) struct_<blah>_init referes to images created during the first-pass of template creation in fslvbm_2_template

3) I’ve answered the GM mask question in the other thread.

Hope this helps,

Kind Regards

Matthew

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 22 May 2019, at 17:08, Yvonne Van Hoecke <[log in to unmask]> wrote:

Dear all,

I am trying to run the FSLVBM analysis and have a few questions. After running the commands from step C - Creating the template: fslvbm_2_template among the segmented files, the struc-subdirectory contains other output files. I am unsure of what the _struc_JAC_nl extension is referring to. The image output is quite blurry as well. I would also appreciate some help in understanding what the difference is between the struc_GM_to_T and struc_GM_to_T_init?.

I then ran the last commands from step E1 and E2, and when displaying the statistical maps, it seems like the whole - brain is significant rather than subregions. When looking into my files in the stats directory, the GM mask seems problematic. Rather than having a GM mask, it looks more like a whole - brain mask with the total volume in white.

Look forward to hearing from you,
Many thanks,
Yvonne

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