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Thank you for your response, Douglas!
We have attached a picture of the pial surface over the orig volume where there
is a severe spike. There are underestimations and overestimations - which seem
to include dura - but there aren't always both.
Here is how recon-all appears in our bash scripts:
Recon-all Cross-sectional
while IFS= read -r file; do
if [ -f "$input_dir/$file" ]; then
# Extract timepoint and participant information from the file name
filename=$(basename "$file")
timepoint="${filename:1:1}"
participant="${filename:3:4}"
# Execute recon-all command
"$freesurfer_bin/recon-all" \
-i "${input_dir}${file}" \
-subjid "Z${timepoint}P${participant}" \
-sd "$output_dir" \
-all
fi
done < "$filename"
Recon-all Base Template
# Loop through each line in the file
while IFS= read -r folder_name || [[ -n "$folder_name" ]]; do
# Check if folder exists in input directory
folder_path="$input_dir$folder_name"
if [ -d "$folder_path" ]; then
# Get participant ID
participant="${folder_name:3}"
# Check if the participant has been processed
if [ -n "${processed_participants[$participant]}" ]; then
echo "Participant ${participant} already processed. Skipping."
continue
fi
# Construct -tp options for all time points
tp_options=""
for tp_folder in "${input_dir}"Z*P"${participant}"/; do
if [ -d "$tp_folder" ]; then
tp=$(basename "$tp_folder" | sed -n
's/Z\([0-9]\+\)P'"${participant}"'/\1/p')
if [ -n "$tp" ]; then
tp_options+=" -tp Z${tp}P${participant}"
fi
fi
done
# Run recon-all command
$freesurfer_bin/recon-all \
-base "P${participant}Base" \
${tp_options} \
-sd "${output_dir}" \
-all
# Mark participant as processed
processed_participants[$participant]=1
fi
done < "$filename"
Recon-all Longitudinal
# Loop through cross files
for cross_file in "${cross_files[@]}"; do
# Extract timepoint
cross_folder_name=$(basename "$cross_file")
cross_timepoint="${cross_folder_name:1:1}"
cross_participant="${cross_folder_name:3}"
# Loop through base files
for base_file in "${base_files[@]}"; do
base_folder_name=$(basename "$base_file")
base_participant="${base_folder_name:1:4}"
if [ "$cross_participant" == "$base_participant" ]; then
# Run command
$freesurfer_bin/recon-all \
-long "${cross_file}" "${base_file}" \
-sd "${output_dir}" \
-all
fi
done
done
Best wishes,
Marieke & Manon
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: donderdag 12 december 2024 14:40
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Spiky Brains
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:
1. 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:
1. 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
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