If you have processed the individual data only up until the dtifit, then yes all your FA images are in the native space.

So I would suggest to register your ROI and FA together before doing any further processing.

How had you defined your ROI? Based on an anatomical scan?

If you have an anatomical and your ROI is defined there, I would do the following steps:

1) First check in fslview the orientation of the anatomical scan. It might be rotated related to the standard orientation. If this is the case, then use the fslreorient2std function. If am not sure if this function will work on your ROI too; better read carefully this http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained and ask an fsl expert if you can't find an answer.

2) Align your _ecc image to the anatomical. Check whether the BET or the non-betted image gives better results. You can align the two images by running the following

    flirt -in "*_ecc" -ref "anatomical" -dof 6 -interp trilinear -omat "DTI_to_anat.mat" -out "DTI_in_anat"

3) Run DTIFIT on the "DTI_to_anat" output in order to have the FA image aligned to the anatomical directly. All these steps should be done for each subject separately.

4) Follow the TBSS processing steps to process your FA images as desired.

5) After having completed all the TBSS steps, you should align the ROI to the MNI space. There are two ways to do so:

    a) flirt -in "anatomical" -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -dof 12 -interp trilinear -omat "anat_to_MNI.mat" -out "anat_in_MNI"

        flirt -in "ROI" -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -applyxfm -init "anat_to_MNI.mat" -interp nearestneighbour -o "ROI_in_MNI"

    b) Since in TBSS the transformation matrices to MNI have been already calculated, you can use these directly. You get these files after running tbss_2_reg

        flirt -in "anatomical" -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -applyxfm -init "*_to_target.mat" -interp trilinear -o "anat_in_MNI"

        flirt -in "ROI" -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -applyxfm -init "*_to_target.mat" -interp nearestneighbour -o "ROI_in_MNI"

6) I would expect intersubject variability in the ROI definition, so if you want to run randomise in your data you should create a "mean" ROI image. Then you case call randomise with this mean ROI as mask.

7) You can get the mean FA value inside your ROI for each subject separately. Then run statistics on these values, but you would lose all spatial information and power in your analysis.

Best regards,

Vasilis

On 6 January 2015 at 09:20, Anupa AV <[log in to unmask]> wrote:

Dear Vasilis,

Thanks a lot for your quick reply. I created all FA images using the follo. step.

 eddy current correction

2. created brain mask

3. BET wih Fractional intensity = 0.3

4. DTI model in FDT using DTIFIT (the output of this step (FA image) is what I am planning to use)

So my images are not in MNI space right now (I guess, I am right!!)

SO straight away, I created the mask on the native T1W image.

The rest of the steps, which you mentioned, I'll try it out and get back to you.

Thanks a bunch for your input.

On Monday, January 5, 2015 6:42 PM, Vasilis M. Karlaftis <[log in to unmask]> wrote:

Dear Anupa (?),

First of all, in which space is your ROI? Have you processed it at all?

I guess that your FA image is in the MNI space if you followed the TBSS processing. Also, your original ROI image should be in the subject's native space but acquired in a different run than the DTI acquisition. Did you have an anatomical scan before the MRS? If yes, then you can use "flirt" command to align that anatomical scan to the MNI space. Then you can use this transformation matrix to transform your ROI from the native space to the MNI and thus be aligned with the FA image. Just remember to use "nearestneighbour" interpolation for the ROI, since you want to preserve the binary values.

It might be sensible for you to wait an expert's input on this, since it could be better to register first both the DTI and MRS scans in the same anatomical image before doing any further processing.

After having done the above registration, getting the FA value from this areas is easy. If you need all the skeleton voxels that fall inside your ROI, then run:

fslmaths "ROI" -mul mean_FA_skeleton_mask "output"

And you can use that output as a mask for randomise call.

or if you want the mean FA value inside your ROI, then run:

fslmeants -i all_FA_skeletonised -m "output_from_fslmaths" -o mean_FA_in_ROI.txt

Hope that helps.

Best regards,

Vasilis

On 5 January 2015 at 05:57, Anupa AV <[log in to unmask]> wrote:

Dear FSL experts,

I'd like to get some tips on  how to perform TBSS using a ROI analysis method.

The objective of my experiment is to integrate MRS and DTI. I've a voxel of size 20*20*20 in the frontal region.

Can any one please clarify my follo. doubts..

1. How to place ROI on individual FA image?

2. How to measure the  FA value from the region of interest that was placed on the FA image.