Total intracranial volume too small in FreeSurfer
Lea
Hello everyone,
Our research group is planning to use the structural data from the HCP-Young Adults dataset for a machine learning study, but we have run into an issue with FreeSurfer preprocessing.
We downloaded the unprocessed T1-weighted structural MRI data from HCP and processed them using the recon-all pipeline in FreeSurfer without any errors. However, the resulting overall brain volume (total intracranial volume) is considerably smaller than in other comparable datasets. This makes the HCP dataset unusable for our study.
We ran the raw-data quality checking tool MRIQC (Esteban et al. 2019, Scientific Data) on these data and got the error ”Detected hat mask was too small; Detected a zero-filled frame, has the original image been rotated?” We didn’t have this error on any comparable dataset.
We are now wondering: Is this an issue of the raw data or FreeSurfer? Does the HCP dataset require a specific mask or specific settings in FreeSurfer?
If you have experienced similar issues or have any thoughts on the above, we’d greatly appreciate your input.
Thank you for your help!
Lea
Glasser, Matt
You should be using the HCP preprocessed results, not raw data.
Matt.
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Harms, Michael
How do your ICVs from your independent run of FS compare to what we’ve generated? (The FS stats are available for HCP-YA on ConnectomeDB).
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Michael Harms, Ph.D.
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Associate 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
From: "Glasser, Matt" <glas...@wustl.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, December 9, 2021 at 8:18 AM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] Total intracranial volume too small in FreeSurfer
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Lea
Hi Matt and Michael,
Thank you both for your quick responses in December. The issue was indeed that we were preprocessing the data ourselves.
We have now downloaded the FS data preprocessed by HCP and we are trying to replicate the HCP FS pipeline to establish whether the output is comparable to the other datasets we are using in our project. We noticed that the documentation says to ignore that the GitHub script specifies FS version 5.3 and install 6.0 instead (https://github.com/Washington-University/HCPpipelines/wiki/Installation-and-Usage-Instructions#installation).
Could you please clarify if this means that the FS data we downloaded were preprocessed using v6?
If this is relevant, we downloaded the file “Extended FreeSurfer Data” (unrestricted_hcp_freesurfer.csv) from the “Quick Downloads” section of the WU-Minn HCP Data resource page on ConnectomeDB.
Thank you in advance for your help.
Kind regards,
Lea
Glasser, Matt
HCP-YA was processed with 5.3 and HCP Lifespan with 6.0.
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