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Dear Paul, I want to find out DMN in single subject rsfMRI. I have done analysi by using melodic and I got all necessary out put files including "melodic_IC_hr.nii.gz" file. There are 29 volumes of images are present in the file which shows activities in different regions. By using WFU_PickAtlas I have created a single mask image which includes multiple rois (DMN). By using fslmaths command I have created threshold mask from the mask created earlier. In fsl view it appears fine. Further I want to know how to apply this mask so that I will get only DMN. (Just want to see dmn in single subject rsfMRI). Thanks Ramesh On Mon, Jun 29, 2015 at 9:44 PM, paul mccarthy <[log in to unmask]> wrote: > Hi Ramesh, > > It is not clear to me exactly what you are trying to do. Are you just > interested in these two scans from a single subject, or is this part of a > larger (multi-subject) study? > > Thanks, > > Paul > > > > > On 27 June 2015 at 11:21, Ramesh Babu <[log in to unmask]> wrote: > >> Dear Paul, >> >> Earlier I had a doubt about the activities seen in my data set. After >> spending some time in FSL view, now I came to know how to look at different >> volumes of the maps. >> >> I have 2 rsfMRI scans, one meditators and one control scans. I have >> analysed separately in melodic as mentioned in the manual and obtained >> transformed map. By looking through FSL view, I found activities in the DMN >> area. The amount of the activity (size of the BOLD activity) is different >> in meditators and control. >> >> Should I create mask related to DMN? Is it necessary for single subject >> analysis? If it is necessary plz guide me how to create mask? >> >> Thanks >> Ramesh >> >> >> >> Since it is single subject analysis I didn't to any statistical analysis. >> Should I create ROI mask to define DMN network in these areas? >> >> On Fri, Jun 26, 2015 at 3:27 AM, Ramesh Babu <[log in to unmask]> >> wrote: >> >>> 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 >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >