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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] <mailto:[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] <mailto:[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 <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] <mailto:[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 >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the FSL list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1> >>> >>> >>> To unsubscribe from the FSL list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1> >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1> > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1> ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1