Hi Mihaela,
it should still work, but may require more edits than with adults (e.g.
if head size changes, the skull strip may differ a lot across time
points. We keep it fixed in the base by computing the union, but that
may be too large for some earlier time points, so you may have to edit
them in the long etc.).
Best, Martin
On 05/28/2015 11:54 AM, Mihaela Stefan wrote:
Dear Martin,
I'm pitching in since this topic concerns me as well.
We are collecting structural data for a longitudinal study with
adolescents. The youngest is 13 years old at baseline and the mean age
is around 16. We will collect 3 follow-ups with a gap of 1.5 - 2
years. The adolescent brain is still in the process of growing but not
that dramatically as at 4.
Can we use the longitudinal stream?
Thanks!
Mihaela
On Thu, May 28, 2015 at 11:13 AM, Clara Kühn <cku...@cbs.mpg.de
<mailto:cku...@cbs.mpg.de>> wrote:
Hi Martin,
thanks for your quick reply. I was indeed referring to the quality
check. I guess I interpreted that incorrectly. With the children
data "inspecting" almost always means "editing".
I also took a look at the cheat sheet again. I've been mulling it
over and my best idea so far is to
1. check/ edit the crosses for control points and rerun
autorecon2-cp -autorecon3 since those get transferred to the long
directly
2. check the base and edit the brainmask (eg taking out blood
vessels and tentoral membrane or cloning voxels if necessary)
since it gets transferred to the long directly
3. check the base and edit the wm mask and rerun -autorecon2-wm
-autorecon3 in the base command
4. check the longs and hope everything is fine :)
We measured the 4 year olds with a gap of 3 weeks between scans
with the assumption that their heads won't grow considerably
within 2 months time. What do you think?
Cheers, Clara
----- Ursprüngliche Mail -----
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@nmr.mgh.harvard.edu>>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Gesendet: Donnerstag, 28. Mai 2015 16:45:57
Betreff: Re: [Freesurfer] what order for longitudinal edits
Hi Clara,
how to edit depends a lot on the type of edit. The general rule is to
edit as early as possible. In some edits, there is shortcuts (e.g.
start
with base, then check long and skip the cross). Take a look at the
Cheat
Sheet on the first link. Also usually there is no need at all to edit
the longs, as the edits in cross and base should fix everything
sufficiently. So in the case of a shortcut (editing base, skipping
cross) you only need to edit 1 run (the base) per subject, not all 3
time points.
I also cannot find the contradiction in the first page. Where does it
say to start editing with the longs, then go backwards? That would
certainly be wrong for editing. Can you please point me to that, so I
can fix it (if it is there). Maybe you confused this with QC (quality
check) which you could do backwards to save time. E.g. if the
longs are
look great, no need to check base and cross.
"QC from back to front (long -> base -> cross), once you find where
problems occur, edit from front to back (cross -> base -> long)."
Cheers, Martin
P.S. probably more important, I doubt that the longitudinal stream
will
work well on 4-year olds. The basic assumption is that head size does
not change, so if that is approximately true, it could work (e.g.
short
time intervals). Otherwise you may run into lot's of editing problems
and it may be easier to just use the cross sectionals in your analysis
(at the cost of increased measurement variability).
On 05/28/2015 10:19 AM, Clara Kühn wrote:
> Dear Freesurfer Experts,
>
> I'm working with the structural data of 4-year olds which we
measured 3 times to asses changes in cortical thickness.
> During the preprocessing I've found some contradicting
information on how to best edit the longitudinal data. On this
site https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
it says to edit stuff as early as possible. However, on the same
site it says to start with the longs, then the base and then the
cross. And on this site
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#FsTutorial.2BAC8-LongitudinalTutorialfreeview.EditingLongitudinalData
it says to check the base first and then the longs.
> I am utterly confused as to how I can edit my data most
efficiently because I have a lot of it (100 children, 3 scans each).
>
> To me, it is also unclear at which point I can edit the long and
rerun the recon process partially (eg. with the -wm flag) and when
it is necessary to go back to the base...
>
> I am very thankful for any kind of revelation on these matters :)
> Cheers,
> Clara Kühn
>
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--
Dr. Martin Reuter
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652 <tel:%2B1-617-724-5652>
Email:
mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>
reu...@mit.edu <mailto:reu...@mit.edu>
Web : http://reuter.mit.edu
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--
Dr. Martin Reuter
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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