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:


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