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Dear Dr. Greve & FS experts,
Thank you so very much for your advice and assistance. I am so grateful for
your help. Which portion(s) of the pipeline was/were not clear? If it would
help, I would be more than happy to try to clarify them further.
Regarding my pipeline, is this what you mean? (see below)
When I use -autorecon3, do I also need to use the "-keep" flag (saw something
about that in the documentation?)?
I first run the initial recon-all:
$recon-all -i <input image> -s <subjID> -sd <subjects_dir> -wsthresh 10 -gcut
Next, I open brainmask.mgz in FreeView and edit out the remaining dura mater
(not already removed by gcut) by hand, overwriting the old brainmask.mgz with
this new, edited brainmask.mgz:
I then run multiple second iterations of recon-all, creating multiple versions
of gm/wm segmentation:
$recon-all -autorecon2-cp -autorecon3 -s <subjID> -sd <subjects_90> -seg-wlo 90
$recon-all -autorecon2-cp -autorecon3 -s <subjID> -sd <subjects_80> -seg-wlo 80
$recon-all -autorecon2-cp -autorecon3 -s <subjID> -sd <subjects_70> -seg-wlo 70
$recon-all -autorecon2-cp -autorecon3 -s <subjID> -sd <subjects_60> -seg-wlo 60
$recon-all -autorecon2-cp -autorecon3 -s <subjID> -sd <subjects_50> -seg-wlo 50
$recon-all -autorecon2-cp -autorecon3 -s <subjID> -sd <subjects_40> -seg-wlo 40
In FreeView, I then visually assess the image/segmentation produced by each
seg-wlo threshold to select the threshold that most optimally segmented the
gray and white matter. I save that to a new subjects directory folder; this new
subjects directory's folder is specified "SELECT" ("subjects_SELECT").
Calculate LGI:
$recon-all -s <subjID> -sd <subjects_SELECT> -localGI
Final qcache:
$recon-all -s <subjID> -sd <subjects_SELECT> -qcache
Thank you!
Emily Harriott
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Sunday, September 25, 2022 12:17 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] confirmation of processes/commands used in full
processing pipeline
On 9/20/2022 5:01 PM, Harriott, Emily M wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I hope this email finds you all doing well. I'm a second-year doctoral student
(and beginner FreeSurfer user) trying to use FreeSurfer to segment gray and
white matter in 90 T1 images of children/adolescents (with reading disorders,
Neurofibromatosis type 1, and typically developing) for a project; I have two
questions about processing these images, and I would be so very grateful to
receive some thoughts/suggestions/advice etc. from some FreeSurfer experts such
as yourselves.
I ran recon-all on each of those 90 images, but one single run of recon-all
left too much dura in the gray matter segmentation and too much white matter
out of the white matter segmentation (the amount of white matter left out
varied depending on the intensity contrast of each image). To fix the dura/gray
matter issue, I re-ran recon-all using the -gcut flag and edited out by hand
the remaining dura; this seemed to help. To fix the white matter issue, I tried
adding control points and adding white matter voxels and re-running recon-all;
this unfortunately did not seem to help, as control points led to worse
segmentation and the added white matter voxels had minimal to no effect.
So, after some experimentation, I have created a full processing pipeline to
use on my data. But, before I apply it to all 90 images, I wanted to confirm
with you all experts that this will 1) work and 2) do what I want it to do.
Question 1: If I process my data in FS 7.2.0, can I go back and analyze it
using QDEC in FS 6.0.0? Or do I have to process it in 6.0.0 to use QDEC?
Yes, that is fine, though keep in mind that we are not supporting qdec any
more.
Question 2: Here is my pipeline (see below). Will this work? Will it do what I
want it to do? Do you have any suggestions? I'm a beginner; is there anything I
should be careful of or watch out for that I don't know about? After some
experimentation on a subsample, this pipeline appears to work, but I really
want to ensure it is doing what I want it to do and will do that consistently.
I did not follow your pipeline description entirely. What you have below looks
like it will do what you want it to do, but I'd change a few things. First, you
need to add -autorecon3 so that it completes the process. You can also use
-autorecon2-cp instead of -autorecon2 (this will skip the most time consuming
part). Finally, I would not run -qcache until after you are satisfied with the
results (you can/should run recon-all with just the -qcache flag)
For one subject....
I first run the initial recon-all (with some flags).
$recon-all -i <input image> -s <subjID> -sd <subjects_dir> -wsthresh 10 -gcut
-qcache
Next, I open brainmask.mgz in FreeView and edit out the remaining dura mater by
hand. When I save this new brainmask.mgz, I overwrite the old brainmask.mgz
with this new edited brainmask.mgz.
I then run multiple second iterations of recon-all, allowing me to use
different seg-wlo thresholds (seg-wlo thresholds of 40, 50, 60, 70, 80, 90 are
applied to each image).
The multiple second iterations of recon-all are:
$recon-all autorecon2 -s <subjID> -sd <subjects_90> -seg-wlo 90 -qcache
$recon-all autorecon2 -s <subjID> -sd <subjects_80> -seg-wlo 80 -qcache
$recon-all autorecon2 -s <subjID> -sd <subjects_70> -seg-wlo 70 -qcache
$recon-all autorecon2 -s <subjID> -sd <subjects_60> -seg-wlo 60 -qcache
$recon-all autorecon2 -s <subjID> -sd <subjects_50> -seg-wlo 50 -qcache
$recon-all autorecon2 -s <subjID> -sd <subjects_40> -seg-wlo 40 -qcache
(Note that I have 6 distinct subjects_?0 folders for 6 distinct seg-wlo values)
In FreeView, I then visually assess the image/segmentation produced by each
seg-wlo threshold to select the threshold that most optimally segmented the
gray and white matter. I save the subject folder with the optimal seg-wlo
threshold, as determined visually in FreeView by me, to a new subjects
directory; this new subjects directory's folder is specified "SELECT".
I now have measures of cortical thickness, surface area, and volume, but I also
want measures of local gyrification index (LGI).
With MATLAB 2022a active (I'm working on a large computing cluster, so I have
to activate MATLAB/2022a as a module), I run the LGI recon-all.
$recon-all -s <subjID> -sd <subjects_SELECT> -localGI -qcache
I then obtain the measurements of LGI. To run this line, I also have a .bashrc
file in my subjects_SELECT folder that has one line: MEASURE1 = pial_lgi.
$recon-all -s <subjID> -sd <subjects_SELECT> -measure pial_lgi -qcache
Then the data go into QDEC and I should be able to analyze from there.
Any confirmations/denials, suggestions, or advice you all have would be so very
greatly appreciated.
Thank you so very much!
Emily Harriott
Doctoral Student, Vanderbilt University
Nashville, TN
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