Hi Victor
for each subject I think you want to run:
set mdir=$SUBJECTS_DIR/$subject/mri
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \
-lta $mdir/transforms/cc_up.lta $subject
cp aseg.auto.mgz aseg.mgz
then run recon-all from normalization2 forward (check the recon-all -help
for these steps)
cheers
Bruce
On Tue, 7 Jan 2014, Victor Kovac wrote:
Hi Bruce,
I ran recon-all -autorecon2-cp -autorecon3 -s MPS1036-1 but, again, this did
not affect the pial or wm surfaces. I have attached the recon-all.log in
case that would be helpful in diagnosing the issue.
Any advise would be greatly appreciated.
Thanks!
Victor
On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Victor
you can look in the recon-all -help and run the stages that are
after mri_ca_label. Not sure why -make all didn't work, perhaps
Zeke and/or Nick can comment?
Bruce
On Thu, 2 Jan 2014, Victor Kovac wrote:
Dear Bruce,
A few weeks ago you made code mods to
mri_em_register and got recon-all to
process a subject of mine, MPS1036-1. You sent me
the new
aseg.auto_noCCseg.mgz and told me to run recon-all
-make all -s MPS1036-1.
I did this but I get the message
make: Nothing to be done for 'all'
and when I visualize the segmentation with tkmedit,
there appears to be no
change to the pial or wm surfaces.
Could you please advise?
Thank you.
Victor
On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
if you rename aseg.auto_noCCseg.new.mgz to be
aseg.auto_noCCseg.mgz
then run:
recon-all -make all -s MPS1036-1
you should be all set
Bruce
On Mon, 9 Dec 2013, Victor Kovac wrote:
I was hoping to MPS1036-1. I only got
aseg.auto_noCCseg.new.mgz. Thank you
for looking into MPS2002-3 -- it is
quite the brain.
And somehow, with all
those morphological abnormalities, this
subject has
an IQ of 130. Very
strange.
Thanks,
Victor
On Mon, Dec 9, 2013 at 2:03 PM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
which one? I'm still messing with
MPS2002-3 in
my spare time
On Mon, 9 Dec 2013, Victor Kovac
wrote:
Hi Bruce,
Is there a way for you to
send the
subject(s) you
analyzed to me? I know
it's too big for email, but
could you
possibly
upload it to GoogleDrive?
Thanks!
Victor
On Wed, Dec 4, 2013 at 3:40
PM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
p.s. the other thing I
did was run
the graph
cut skull
stripping, which
removed a bunch
of extraneous
stuff
On Wed, 4 Dec 2013,
kovac...@umn.edu wrote:
Hey!
Victor Kovac
(kovac...@umn.edu)
has uploaded
some files
for you at the
Martinos Center
FileDrop:
-> MPS2002-3.zip (292.12
MiB)
<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=55xjt9pflsi>
-> MPS2017-1.zip (264.15
MiB)
<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=ak4v31bzu4p>
Also, they left this message
for you:
Hi Bruce,
Here are the two subjects
with
ventriculomegaly that
are causing
the worst issues. The worst
segmentation
in
MPS2002-3 is in the
superior frontal (slices
150-180) and
parietal
(slices 50-95)
cortical areas; this may be
due to the
numerous
dilated
Virchow-Robin spaces in his
brain, which
is another
neuropathological feature of
this
disease.
Thanks!
Victor
Please be aware, your upload
will expire
on December
31st. If
you'd like to download these
files, feel
free to use
the link
below:
http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep
Cheers,
The NMR Team
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