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Dear Paul, Thank you. I have learned a lesson that I should not copy paste in the terminal. Thanks In the downloaded data (short.nii, 100 volumes) I saw some activity in the DMN. But in my data (has 120 volumes) it shows activity only in the temporal region. Should I change the threshold to .5 (default value) in the post stat window of melodic? or any other suggestion? Thanks Ramesh On Fri, Jun 26, 2015 at 2:11 AM, paul mccarthy <[log in to unmask]> wrote: > Hi Ramesh, > > This looks like a copy+paste issue again - try typing the fslview command > manually, and it should work. > > Cheers, > > Paul > > On 25 June 2015 at 19:01, Ramesh Babu <[log in to unmask]> wrote: > >> Dear Paul, >> When I type "fslview $FSLDIR/data/standard/MNI152_T1_2mm >> melodic_IC_hr.nii.gz ‐l "Red‐Yellow" ‐b 5,10" it opens the fsl view window, >> but it shows missing image/header. Then after clicking OK 3-4 times, it >> opens the image. Should I ignore this or is there any solution for this >> problem? >> >> Thanks >> Ramesh >> >> On Wed, Jun 24, 2015 at 9:29 PM, paul mccarthy <[log in to unmask]> >> wrote: >> >>> Hi Ramesh (sorry for getting your name wroing previously!), >>> >>> That is a complex question - there are many ways to identify the DMN. >>> Probably the most common would be to use MELODIC on your data, and find the >>> component which most closely resembles the DMN. >>> >>> You could use the component from the Smith et. al. 2011 study as a >>> template: >>> >>> http://www.fmrib.ox.ac.uk/analysis/brainmap+rsns/ >>> >>> Cheers, >>> >>> Paul >>> >>> On 24 June 2015 at 16:45, Ramesh Babu <[log in to unmask]> >>> wrote: >>> >>>> Dear Paul, >>>> Now I got the result. Earlier I have made a mistake by typing "\" in >>>> the command line. After removing this, I got the result. I need one more >>>> help from you. How to identify DMN by using fsl atlas. is there any other >>>> way to find out DMN? >>>> >>>> Thanks for your help. >>>> Ramesh >>>> >>>> >>>> On Wed, Jun 24, 2015 at 8:39 PM, Ramesh Babu < >>>> [log in to unmask]> wrote: >>>> >>>>> Dear Paul, >>>>> >>>>> Still I am facing the same problem. >>>>> >>>>> [fsl@fslvm6 filtered_func_data.ica]$ flirt -in melodic_IC -ref >>>>> $FSLDIR/data/standard/MNI152_T1_2mm \ -out melodic_IC_hr -applyxfm -init >>>>> ../reg/example_func2standard.mat >>>>> >>>>> Unrecognised option >>>>> >>>>> [fsl@fslvm6 filtered_func_data.ica]$ >>>>> >>>>> Please see the list of file generated after first step which I have >>>>> given below. >>>>> [fsl@fslvm6 filtered_func_data.ica]$ ls >>>>> >>>>> eigenvalues_percent mean.nii.gz melodic_ICstats melodic_Tmodes >>>>> log.txt melodic_FTmix melodic_mix report >>>>> mask.nii.gz melodic_IC.nii.gz melodic_PPCA stats >>>>> >>>>> [fsl@fslvm6 filtered_func_data.ica]$ >>>>> >>>>> Even after typing (not copy pasting), I am getting the same error >>>>> message (Unrecognized options). >>>>> >>>>> It will be very helpful for me if you provide the solution for it. >>>>> >>>>> Thanks >>>>> Ramesh >>>>> >>>>> On Tue, Jun 23, 2015 at 3:31 PM, paul mccarthy < >>>>> [log in to unmask]> wrote: >>>>> >>>>>> Hi Ramesh, >>>>>> >>>>>> Did you copy+paste the flirt command from the web page? Instead, >>>>>> manually type out the command, and see if that works. >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Paul >>>>>> >>>>>> On 23 June 2015 at 07:32, Ramesh Babu <[log in to unmask]> >>>>>> wrote: >>>>>> >>>>>>> Dear FSL member, >>>>>>> >>>>>>> I have downloaded example data set for resting state fMRI analysis >>>>>>> in FSL. I am following step by step procedure mentioned in the manual >>>>>>> "Model Free FMRI Analysis Practical-Resting State data analysis >>>>>>> (Optional)". I am getting an error which I have pasted below. >>>>>>> >>>>>>> "[fsl@fslvm6 filtered_func_data.ica]$ flirt ‐in melodic_IC ‐ref >>>>>>> $FSLDIR/data/standard/MNI152_T1_2mm ‐out melodic_IC_hr ‐applyxfm ‐init >>>>>>> ../reg/example_func2standard.mat >>>>>>> >>>>>>> Unrecognised option >>>>>>> >>>>>>> [fsl@fslvm6 filtered_func_data.ica]$" >>>>>>> >>>>>>> I didn't understand why it shows unrecognized option. Once I get DMN >>>>>>> in this sample data then I will proceed scanning in similar way for my >>>>>>> project. >>>>>>> >>>>>>> Since I am not familiar with scripting, it will be helpful for me if >>>>>>> you give step by step usage of FLIRT GUI. >>>>>>> >>>>>>> Thanks >>>>>>> Ramesh Babu >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >