Hi Jintao,

The difference comes from the fact that the MNI template I used is 256 x 256 x 256, which was obtained by passing the FSL MNI152 template through the FreeSurfer recon-all pipeline. Therefore even though the header information are different, they are still in the same space.

You can convince yourself by using freesurfer's freeview to load both the MNI template I provide and the MNI template from FSL:

>> freeview FSL_MNI152_FreeSurferConformed_1mm.nii.gz $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

You should observe they are in perfect alignment (although the values have been altered by recon-all intensity normalization process). If the different headers bother you, what you can do is to use freesurfer's function mri_vol2vol to re-interpolate the volume. For example:

>> mri_vol2vol --mov FSL_MNI152_FreeSurferConformed_1mm.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o new_volume.nii.gz --no-save-reg

Regards,
Thomas



On Thu, Dec 31, 2015 at 2:59 PM, <shengjt2014@163.com> wrote:

Hello Professor Thomas，

 

Thank you for your reply so quickly.

 

I download the zip files on the webside you gave me, and the images look like normal, but when I checked the header information, I found some differences with common MNI images.

 

Could you see the following pictures and notice the regions with blue lines circled.

 

           

 

Excuse me to bother you again.

Best wishes,

Jintao

 

 


发件人: Thomas Yeo
发送时间: 2015年12月31日 11:46
收件人: shengjt2014@163.com
抄送: freesurfer
主题: Re: about functional ROIs

 

Hi Jintao,

 

This might be a header error in the original files. The error is not apparent in the FreeSurfer or FSL environment, but might be problematic with mricron (completely my fault).

 

Can you try the files from this zip file instead: https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation_MICRON.zip (courtesy of Chris Rorden).

 

Please let me know if this resolves your issues.

 

Regards,

Thomas 

 

On Thu, Dec 31, 2015 at 10:23 AM, <shengjt2014@163.com> wrote:

 

Dear Professor Yeo,

 

My name is Sheng Jintao, and I am a master in China.

Recently, I download the ‘Resting State Cortical Parcellation in nonlinear MNI152 space’ in https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011, But when I opened images and found they are very stange. Just like this sectional drawing. And I don’t know why, therefore, I would love to consult you.

Thank you, and I look forward to hearing from you.

 

Best wishes,

Jintao