Germaine Chew

• Undergraduate
• Temasek Polytechnic

Dear all,

I analyzed some FA and MD data with TBSS & voxelwise stats and found non-significant findings when p<.05.

I was wondering if there is a way to tell if the analyzed data is really non-significant or is there something that went wrong during the preprocessing (although I highly doubt it as I checked the terminal logs and data).

And if it is really non-significant, what are the reasons for the non-significance (aside from the low sample size).

I have 27 (14 experimental, 13 control) subjects in total.

Any help is appreciated.

Thanks!

Hi guys,

I'm thinking of analysing TBSS on the cerebellum and I was wondering if it is possible to extract FA values out from it?

Thanks for the help!

Hi all,

I'm trying to run FSL(GUI) FUGUE on eddy-corrected DTI data but I'm unable to generate a warp from it. I get files looking like this (see photo attached).

May I know if there is any terminal command that I can use to run FUGUE?

Or should I should use FUGUE before the eddy-corrected DTI data? And if I were to do this step, I understand that it will affect my bvecs. So how do I go about acquiring the new bvecs; given that the bvecs file is the file one gets when converting DTI DICOM to NIFTI data.

Thanks!!

Hi Guys,

So I have tried running FSL eddy using both GUI and terminal. 

From GUI, I got data.nii.gz and data.ecclog.

And from terminal, I got data.nii.gz, data.eddy_movement_rms, data.eddy_outlier_map, data.eddy_outlier_n_sqr_stdev_map, data.eddy_outlier_n_stdev_map, data.eddy_outlier_report, data.eddy_parameters, data.eddy_post_eddy_shell_salignment_parameters, data.eddy_restricted_movement_rms and data.eddy_rotated_bvecs.

I would like to enquire why the files generated will be different and the images generated differs slightly as well too. 

I have two fieldmaps directly converted from DICOM to NIFTI (magnitude image and phase difference image) and I would like to run EPI distortion on the data which I have corrected for eddy currents and subject movement. How do I run it through FSL GUI FEAT Pre-stats? Do i have to first calculate the field map using fsl_prepare_fieldmap?

Hi all,

just a curious question. Why do we need to generate a brain mask of b0 using BET for Eddy?

Hi guys, I have the following information: 

Phase enc. dir. A >> P

Echo spacing 0.84 ms

EPI factor 84

Based on the following, does this mean that my fourth number will be 0.84*0.001*83 which means that my acqpara.txt will be:

0 -1 0 0.06972 

Hi All!

What will happen if you run EDDY in FSL FUI without acqpara.txt and index.txt? I have tried running it without acqpara.txt and index.txt and the data.nii.gz is still generated.