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Hi Paul,

I am actually doing the group analysis in Freesurfer, So I was viewing them on the surface using the registration matrices computed first at the FSL level and converted to Freesurfer formats (hence I really want to avoid redoing registrations). The command I was using was 
tksurfer ES_PRJ1 lh inflated -annot aparc.annot -ov ./Run1/Read1+.gfeat/cope11.feat/stats/zstat1.nii.gz -ovreg ./Run1/Read1+.feat/reg/freesurfer/std2anat.reg.dat -fthresh 3.09 -fmid 4 -fslope 1
What I was seeing was 180 degree rotation in the way data is shown. 
I understand that you cannot view the results this way as the cortical surface files are not present. 

So I just checked the results on FSL view, the way I tried to view is open the standard.nii.gz file under FEAT/reg folder and add GFEAT/cope5.feat/stats/zstat1.nii.gz. This works for original GFEAT which I had done, but for the GFEAT done after the post-stats analysis only, comes back with an ‘incompatible overlay’ error. I also notice that GFEAT/report_reg.html is not having any relevant information, so is inputregs folder missing.   

Thanks very much.
Mariam.





On 13 Feb 2015, at 10:54, paul mccarthy <[log in to unmask]> wrote:

Hi Mariam,

I'm having trouble finding anything wrong with your second level analysis (.gfeat) results - it all seems to line up with the first level .feat results.

Can you clarify exactly which image(s) you were looking at that were incorrectly oriented, and how you were viewing them?

Thanks,

Paul

On Wed, Feb 11, 2015 at 6:17 AM, Mariam Sood <[log in to unmask]> wrote:
Hi Paul,

I have uploaded the folders (Mariam-FSL.zip) to the URL. There is a Readme in it mentioning anything non-standard I have done. 
Much appreciate your help.

Many thanks,
Mariam.

On 10 Feb 2015, at 16:36, paul mccarthy <[log in to unmask]> wrote:

Hi Mariam,

Could you please upload your .gfeat folder, and one of the first level .feat folders to this URL?

https://oxfile.ox.ac.uk/oxfile/work/extBox?id=214687855CEEB78A7E

Thanks,

Paul

On Mon, Feb 9, 2015 at 3:41 PM, Mariam Sood <[log in to unmask]> wrote:
Dear FSL experts,

I am doing a partial post-stats analysis to my data. I had selected ‘Copy original FEAT directory for post-stats/registration’ in the misc tab. I did not want to loose my original registration, hence turned off the registration. Post-stats works fine (during the process of backing up, the software was complaining about a few missing files such as design.lev which is never in my FEAT directory. I worked around the problem by creating dummy files). After post-stats, individual run’s FEAT results looks fine.

Next I did a GFEAT using the newly created FEAT folders, and there seems to be something not right with the registration. The new GFEAT folder doesn’t seem to have inputregs folder, and the data is oriented in the opposite way. If I look at the GFEAT results using my original registration, what should be seen at the occipital lobe is at frontal lobe and vice versa.

I tried to edit design.fsf files in the new FEAT folders (after individual runs were processed) to suggest that they had gone through registration, hoping GFEAT process is looking at the registration settings in these files, but that does not seem to fix the problem.

I am happy to edit  any settings in the files rather than redo registration.

Please advice.

Many thanks,
Mariam.

Mariam Sood
PhD Student.
Birkbeck, London.