Problem in “dwifslpreproc”

[Li_Xue]

I am trying to run dwifslpreproc by “dwifslpreproc dwi_denoised.mif dwi_denoised_preproc.mif -rpe_header”

but the results shows: sampling of b=1000 shell is strongly asymmetric; distortion correction may benefit from use of: -eddy_options " … --slm=linear …

my bval: "0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 "

could you please give me some advice about how to address this problem?
Thanks a lot

[jdtournier]

This is typically just a warning, it shouldn’t prevent the command from executing. What it says is that your DW scheme is asymmetric, a problem explained in more detail on the FSL EDDY wiki page. In such cases, it’s recommended to run eddy with the --slm=linear option (enable linear second-level modelling), which you can do by adding -eddy_options " --slm=linear" to your dwifslpreproc command.

[Li_Xue]

Thanks for your feedback.
I got another question about brain Segmentation.
I tried to segment the brain based on the template of “Schaefer2018_200Parcels_7Networks…” (From
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/project_to_individual)

I tried to used the code from above link. but there is something wrong with my results. please see below:

1. Step1

mri_surf2surf --hemi lh \
  --srcsubject fsaverage \
  --trgsubject sub-CON02_recon \
  --sval-annot lh.Schaefer2018_200Parcels_7Networks_order.annot \
  --tval sub-CON02_recon/label/lh.Schaefer2018_200Parcels_7Networks_order.annot

mri_surf2surf --hemi rh \
  --srcsubject fsaverage \
  --trgsubject sub-CON02_recon \
  --sval-annot rh.Schaefer2018_200Parcels_7Networks_order.annot \
  --tval sub-CON02_recon/label/rh.Schaefer2018_200Parcels_7Networks_order.annot

I can get good results in individual surface space:

.

2. Step2

mri_aparc2aseg --s sub-CON02_recon --o seg_yeo200.mgz --annot Schaefer2018_200Parcels_7Networks_order

Then I got parcellation in volume space “seg_yeo200.mgz” :

3. Step3
But the problems occurs when I tried to excute the following code:

 labelconvert seg_yeo200.mgz /usr/local/freesurfer/subjects/Schaefer2018_200Parcels_7Networks_order_LUT.txt \
  /home/xueli/mrtrix/mrtrix3/share/mrtrix3/labelconvert/fs_default.txt \
  sub-CON02_parcels.mif

The sub-CON02_parcels.mif was shown as follows:

The segmentation is really bad, it can not refelct the segmentation of whole brain. and I think there must be something wrong with “LUT.txt” file, but I can not find suitable lookup table. Could you please give me some suggestions about how to creat a suitable lookup table or where can I find the suitable lookup table?

Thanks

Cheers.

Li

[NicDC]

Dear @Li_Xue ,

It does seem to be a problem with the LUT you provide - fs_default will only have the same subcortical (aseg) labels overlapping with the Shaefer2018 LUT. That is why only these are included in the output label file. Since the correct ordered label file is not provided by default, you will need to create this yourself.

All you need to do is to edit the “Schaefer2018_200Parcels_7Networks_order_LUT.txt” file to retain the rows that are a part of the specific atlas. Then delete the column corresponding to the FreeSurfer label IDs and in its place add a column with integers increasing from 1 to the number of rows. Use this file as the second input to labelconvert.

Hope this helps,
Nick

PS: For future reference, it might be easier if you post new questions to a new topic, so that others with a similar issue can find it more easily!

[Li_Xue]

Thanks Nick.

I have obtained the correct LUT file. I upload these files for the people who may meet the same problem with me.
(For the format limitation, I can only upload the pdf file.)

Schaefer2018_200Parcels_7Networks_order.pdf (58.4 KB)
Schaefer2018_200Parcels_7Networks_order_LUT.pdf (71.0 KB)

I used the following code:

labelconvert seg_yeo200.mgz /usr/local/freesurfer/subjects/Schaefer2018_200Parcels_7Networks_order_LUT.txt \
  /usr/local/freesurfer/subjects/Schaefer2018_200Parcels_7Networks_order.txt \
  yeo200_parcels.mif

PS: Thanks for your advice, I will post new questions to a new topic next time.
and could your team increase the variety of format of uploaded files? I found I can not upload the .txt file.

[Li_Xue]

The file yeo200_parcels.mif is shown as follows:

Thanks.

Cheers.

Li

[NicDC]

Glad that it worked,

Have uploaded the text files to a fork here for anyone who needs them.

Nick