Hi - if what you want is to do higher-level analyses in the space of the subject's T1, it may be enough (using FEAT GUI)  to just NOT turn on the "Main structural image", and change the Standard space image selection to your brain-extracted T1?

Cheers.

On 16 Mar 2019, at 08:40, Neji Hyuga <[log in to unmask]> wrote:

Dear Experts,

Can anyone kindly help? I have been stuck in this problem for a very long time and hopelessly looking for a solution.

So, I came across Dr. Jeannette Mumford's tutorial about how to skip feat registration. Her tutorial works, in the case that the data is already registered, so by changing all the .mat  files to FSL's identical matrix ( and using mean_func.nii.gz  as standard.nii.gz), FSL will not crash and nothing will be further registered/interpolated.

In my case, I want to only bypass the registration to MNI and I still want my functional images to be registered on T1 image. For this purpose, I left the following matrices as they are:
example_func2highres_init.mat

example_func2highres.mat

highres2example_func.mat

Then, I changed standard2highres.mat, standard2example_func.mat, highres2standard.mat and example_func2standard.mat to the identity matrix. Finally, I use mean_func.nii.gz  as the standard.nii.gz image. However, the results do not seem correct. 

Could someone tell me what I am doing wrong?

Thanks in advance,

Neji

On Thu, 14 Mar 2019 at 11:00, Neji Hyuga <[log in to unmask]> wrote:

Thank you very much, Taylor. I have been stuck in this problem for a long time.

My steps are as follows:

1. Bet brain the structural image

2. motion correction on functional

3. distortion correction on functional

4. run GLM through the feat

In my registration tab of the feat, I uncheck the registration to the standard space. This runs fine for the first-level analysis, however, when I want to do the second-level analysis I got the following error: "Registration has not been done for all of the FEAT directories that you have selected for group analysis. Please turn on and set up registration".

I believe the problem is happening in the registration because when I  check the registration to the standard space, everything works fine and I have no difficulty in the second-level or third-level analysis.

Best Regards,

Neji

On Tue, 12 Mar 2019 at 07:47, Taylor Hanayik <[log in to unmask]> wrote:

Hi, 

Could you share what the error text is, and elaborate on the steps you perform prior to receiving the error?

Cheers,

Taylor Hanayik


Taylor Hanayik PhD
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]

On 11 Mar 2019, at 17:23, Neji Hyuga <[log in to unmask]> wrote:

Hello Experts,

I am a beginner in using FSL.

I would like to co-register my EPI images to the T1 (so that they will be in the same space, having the same resolution), and do all the subsequent analysis in T1 space, without further normalization to MNI.

This is possible in first level feat analysis but when I want to combine my data in the second level analysis I am getting an error.

Could someone please advice?

Best regards,

Neji

---

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

---

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

---

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve

---------------------------------------------------------------------------

Stop the cultural destruction of Tibet

---

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1