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