This sometimes happens with noisy data. The difference in SNR between
those two scans is a factor of 2. What is your recon-all command line?
Can you send pics of the brain image with the surface overlaid on a
slice with one of the spikes? What does the white surface look like in
those regions? Is it actually grabbing part of the skull or dura?
On 12/12/2024 4:44 AM, Bos, M.G.N. (Marieke) wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
We are completing quality control in FreeView of two longitudinal
datasets (participants age: 9-25) and have noticed that in one dataset
the brains look much more 'spiky' than in the other dataset. More than
half of the brains have some 'spikes', < 10% has severe spikes; the
most obvious ones correspond with both underestimations and
overestimations in frontal regions of the brain (e.g., frontal pole,
rostral middle frontal and superior frontal). The datasets are
collected on two different scanners:
Dataset with the spiky brains:
* Structural MRI data were acquired using a Philips Achieva 3.0
Tesla MRI scanner with a standard whole-head coil. The following
parameters were used: FOV = 224 mm x 178.5 mm x 168 mm; TR = 9.8
ms; TE = 4.6 ms; flip angle = 8 degrees; voxel size = 0.875 mm x
0.875 mm x 0.875 mm. The duration of the anatomical scan was 297.8
s. To reduce head motion, foam inserts were used and a film was
projected on a screen.
Dataset without spiky brains:
* Structural MRI data were acquired using a Philips Achieva 3.0 TX
MRI scanner with a standard whole-head coil. The following
parameters were used: FOV = 250 mm × 196 mm × 170 mm; TR = 7.9 ms;
TE = 3.5 ms, flip angle = 8 degrees, 228 × 177 × 155 slices;
voxel size = 1.1 × 1.1 × 1.1 mm. The duration of the anatomical
scan was 251 s. To reduce head motion, foam inserts were used.
We are not too sure what to do about these. Manual skull stripping,
adjusting the watershed threshold and using control points are not
perfect solutions for various reasons. And we have noticed that the
spikiness is reduced in some brains when the scans are processed in
version 6.0 compared to version 7.3 - but otherwise version 7.3 seems
like the better fit.
We couldn't find anything in the archives, but we wonder - have you
come across this before? Do you have another idea for us to try?
Or is it possible that data from these regions would be (mostly)
unimpacted by the appearance of small, infrequent spikes? If we want
to use global brain measures, do you think Freesurfer gives a reliable
estimation or would you advise us to exclude them from the analyses
due to bad data quality.
We have attached one picture of severe spikes so you know what we
mean. We have started to rate the spikes from 1 (small/infrequent) to
4 (large/frequent).
Thank you in advance for any ideas you can share with us.
Best wishes,
Manon
Marieke
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
