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,PaulOn 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?ThanksRameshSince 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. ThanksIn 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?ThanksRameshOn 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,PaulOn 25 June 2015 at 19:01, Ramesh Babu <[log in to unmask]> wrote:Dear Paul,When I type "fslview $FSLDIR/data/standard/MNI152_T1_2mm melodic_IC_hr.nii.gz ‐l "Red‐Yellow" ‐b 5,10" it opens the fsl view window, but it shows missing image/header. Then after clicking OK 3-4 times, it opens the image. Should I ignore this or is there any solution for this problem?ThanksRameshOn Wed, Jun 24, 2015 at 9:29 PM, paul mccarthy <[log in to unmask]> wrote:Hi Ramesh (sorry for getting your name wroing previously!),That is a complex question - there are many ways to identify the DMN. Probably the most common would be to use MELODIC on your data, and find the component which most closely resembles the DMN.You could use the component from the Smith et. al. 2011 study as a template:Cheers,PaulOn 24 June 2015 at 16:45, Ramesh Babu <[log in to unmask]> wrote:Dear Paul,Now I got the result. Earlier I have made a mistake by typing "\" in the command line. After removing this, I got the result. I need one more help from you. How to identify DMN by using fsl atlas. is there any other way to find out DMN?Thanks for your help.RameshOn Wed, Jun 24, 2015 at 8:39 PM, Ramesh Babu <[log in to unmask]> wrote:Dear Paul,Still I am facing the same problem.[fsl@fslvm6 filtered_func_data.ica]$ flirt -in melodic_IC -ref $FSLDIR/data/standard/MNI152_T1_2mm \ -out melodic_IC_hr -applyxfm -init ../reg/example_func2standard.matUnrecognised option[fsl@fslvm6 filtered_func_data.ica]$Please see the list of file generated after first step which I have given below.[fsl@fslvm6 filtered_func_data.ica]$ lseigenvalues_percent mean.nii.gz melodic_ICstats melodic_Tmodeslog.txt melodic_FTmix melodic_mix reportmask.nii.gz melodic_IC.nii.gz melodic_PPCA stats[fsl@fslvm6 filtered_func_data.ica]$Even after typing (not copy pasting), I am getting the same error message (Unrecognized options).It will be very helpful for me if you provide the solution for it.ThanksRameshOn Tue, Jun 23, 2015 at 3:31 PM, paul mccarthy <[log in to unmask]> wrote:Hi Ramesh,Did you copy+paste the flirt command from the web page? Instead, manually type out the command, and see if that works.Cheers,PaulOn 23 June 2015 at 07:32, Ramesh Babu <[log in to unmask]> wrote:Dear FSL member,
I have downloaded example data set for resting state fMRI analysis in FSL. I am following step by step procedure mentioned in the manual "Model Free FMRI Analysis Practical-Resting State data analysis (Optional)". I am getting an error which I have pasted below.
"[fsl@fslvm6 filtered_func_data.ica]$ 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