ROI analysis

[Aikam Rai]

Hi,

I hope this message finds you well! 

Part 1:

I ran the first three minimal processing HCP pipelines and I was wondering if the following is correct.

In the subject folder I have the following files:

1. /home/user/Projects/ASL/{subject_id}/T1w/T1w_acpc_dc_restore.nii.gz

2. /home/user/Projects/ASL/{subject_id}/T1w/aparc+aseg.nii.gz

I overlaid the files, went through the recon-all logs, and associated publications, but just wanted to confirm that file 2 aligns with file 1, so if I wanted to create brain masks for specific areas with the HCP pipelines specific pipelines, these would be the files to use. I am just a little confused because there are multiple T1 and aparc+aseg files. I am assuming that I would not use the files saved in /home/user/Projects/ASL/{subject_id}/T1w/{subject_id}/mri

Part 2:

I have been able to run the ASL pipeline. I wanted to confirm that the following is correct.

I have the following files:

1. /home/user/Projects/ASL/{subject_id}/T1w/ASL/perfusion_calib.nii.gz. 

2. /home/user/Projects/ASL/{subject_id}/T1w/T1w_acpc_dc_restore.nii.gz.

3. /home/user/Projects/ASL/{subject_id}/T1w/aparc+aseg.nii.gz

Is file 1 registered to file 2? Its seems like they are in the same space when I overlay them but the first file is in 2.5 mm isotropic space and the second is 0.8 mm.

If this is true is the following correct:

1. Change the voxel resolution of file 1 to 0.8 mm (same as file 2 and 3), so that masks can be created.

2. Create region of interest masks using file 3

3. Use the masks on file 1 to get perfusion values for specific regions.

I am looking forward to your response!

Best,

Aikam Rai

[Harms, Michael]

 

Hi,

All the files in T1w/* and T1w/ASL/* should be in alignment/registration with each other (“T1w space”).  They may have different voxel sizes.

 

The files in {subject_id}/T1w/{subject_id}/mri are the unaltered outputs from FreeSurfer itself. 

 

Hopefully Thomas (cc’ed) can chime in on that masks that already available within the ASL pipeline.

 

Cheers,

-MH

-- 

Michael Harms, Ph.D.

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

Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

St. Louis, MO  63110                          Email: mha...@wustl.edu

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[Thomas Kirk]

Hi Aikam,

 

Mike is correct, all the files in T1w will be aligned with each other but not necessarily in the same voxel grid. One way of changing resolution is to make an identity 4x4 matrix and pass that to wb_command -volume-resample (sure chat GPT can suggest other ways). This will change the voxel grid without actually moving the image.

 

I’d suggest resampling the perfusion images onto the aparc+aseg.nii.gz. Resampling segmentation images is fiddly so better to avoid it. Also worth checking freesurfer’s mri_segstats to do the reporting against the segmentation for you, rather than having to make the masks yourself.

 

The HCP ASL pipeline produces tissue masks (T1w/ASL/pvs) but doesn’t provide any more detailed masks, nor at 0.8mm resolution.

 

Hope this helps

Tom

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[Aikam Rai]

Perfect, thank you so much! This really helped. 

Best,

Aikam Rai