Import anatomy from FreeSurfer generated by recon-all-clinical.sh

quraishi · June 25, 2024, 5:33pm

There is a new recon process available since FreeSurfer version 7.4 called recon-all-clinical. The output from this script does not import directly into Brainstorm's "Import anatomy folder" function like the usual recon-all output does, because there is no "T1.mgz." Would anyone be able to update Brainstorm to accommodate the new file names and directory structure? Thank you!

edelaire · June 25, 2024, 6:54pm

Hello,
would you be able to upload the output of freesurfer somewhere so we can do test?

Regards,
Edouard

quraishi · June 26, 2024, 12:11am

Here is an example

Shared for Brainstorm testing

Raymundo.Cassani · June 26, 2024, 1:59pm

@Anand_Joshi any thoughts on this?

edelaire · June 26, 2024, 4:41pm

Hello,

I started a PR here: WIP on recon-all-clinical by Edouard2laire · Pull Request #714 · brainstorm-tools/brainstorm3 · GitHub

The description of the files is here: recon-all-clinical - Free Surfer Wiki

Notably:

native.mgz: input (reconstructed) volume.
synthSR.raw.mgz: raw output of SynthSR (1 mm isotropic MPRAGE) might be better for visualization
synthSR.mgz (brain only version of synthSR.raw.mgz)

Two observation:

Atlases (ASEG) seems to be computed on synthSR.mgz and don't have same dimension as native.mgz or synthSR.raw.mgz. Maybe we can resample to synthSR.raw.mgz (similarly as what is done if we visualize them in FreeView)
The surface don't seems aligned with the volume in brainstorm. I don't have the issue in Freeview

Freeview

image935×569 115 KB
Brainstorm

image1227×660 132 KB

Raymundo.Cassani · June 26, 2024, 10:54pm

Agree, we should be importing this one referece MRI.

With recon-all-clinical the infamous FreeSurfer=>Brainstorm transformation is not needed anymore:

github.com

brainstorm-tools/brainstorm3/blob/6e05b86065189bdc91bf57f2a0759e88d855edb7/toolbox/io/in_mri_mgh.m#L143-L145


      
          isApplyBst = java_dialog('confirm', ['Apply the standard transformation FreeSurfer=>Brainstorm?' 10 10 ...

                                               'Answer "yes" if importing transformed volumes such as T1.mgz in the' 10 ...

                                               'FreeSurfer output folder, or other volumes in the same folder.' 10 10],  'MRI orientation');

This is the result of importing the FreeSurfer folder (auto) without applying FreeSurfer=>Brainstorm, but applying the vox2ras transformation available in the MRI file.

Yes, synthSR.mgz is masked, and the anatomical parcellations are defined for this volume.
Although, synthSR.mgz and synthSR.raw.mgz do not have the same volume size, the 2nd one is a subspace of the first one, so, by trimming synthSR.mgz, we can have the same volume space. Already working on how to identify and compute the extra space to be removed.

Left: "trimmed" ASEG on synthSR.raw.mgz
Right: imported ASEG on synthSR.mgz

edelaire · July 3, 2024, 3:21pm

Hello @quraishi,

The support for recon-all clinical has been added to brainstorm by Raymundo here: Add support for importing FreeSurfer results from 'recon-all-clinical.sh' by Edouard2laire · Pull Request #714 · brainstorm-tools/brainstorm3 · GitHub

You can update your brainstorm and try again

Edouard