Hi Douglas,
I have reported many problems with the skull stripping and resulting issues in
freesurfer. to
summarize:
1. For our structural scans, we have significant pial matter/dura matter
remaining for about 50% of
subjects or more (of a dataset of 350 scans). I have tested using freesurfer's
gcut and other
options, as well as AFNI skull strip, FSL with many options, and even ANTS.
2. We gave up on trying to use surfaces with this dataset, due to the sheer
amount of manual
intervention that would be needed to edit the brains
3. The aseg almost always labels the remaining skull as gray matter, which then
influences the icv
and wbv measurements. W
4. Recently we have decided to try the longitudinal pipeline. Another problem
appears: if a
cross-sectional scan does not have any pial matter (as in, it is one of the few
that as successfully
skull stripped - we call these the "clean" scans) but a template is made from
multiple scans from
this subject. If one of those other tp scans from this subject has any pial
mater remaining, then
the (a) the template will include all of the pial matter and (b) the
longitudinal version of the
"clean" scan now has extra pial matter that gets erroneously labeled as gray
matter, or sometimes
white matter. Attached is a screenshot example of this problem.
I have been trying to solve this for over a year, and I also sent data to
freesurfer over the ftp on
December 1st using the directions on the freesurfer wiki, if you want to take a
look at a single
representative scan with this skull strip issue.
Thanks!
Michelle
----
Douglas N Greve Tue, 19 Dec 2017 15:25:14 -0800
Hi Michelle, sorry about not getting to this before. It looks like Bruce
was helping you out, but he's just left and won't be back until the new
year. To answer your first question, I don't think that v6 performs much
differently on skull stripping than v5.3. What is the nature of the
skull stripping problem? Can you send screen shots?
doug
On Tue, Dec 19, 2017 at 3:47 PM, Michelle VanTieghem
<[email protected]> wrote:
Hi,
I am following up again -- on my prior posts regarding skull strip issues and
whether
using freesurfer 6.0 would improve over freesurfer 5.3 .
I sent the data over the ftp on Dec 1 and would greatly appreciate it if you
could take a
look to see if there is a way to improve the skull strip since we have this
issue with 100+
scans and my attempts to use gcut, and other skullstrip programs, has not
worked.
Thank you,
Michelle
On Fri, Dec 8, 2017 at 12:31 PM, Michelle VanTieghem
<[email protected]> wrote:
Hi,
I am just following up on my prior posts regarding skull strip issues and
whether using
freesurfer 6.0 would improve over freesurfer 5.3 .
I sent the data over the ftp and would greatly appreciate it if you could take
a look to
see if there is a way to improve the skull strip since we have this issue with
100+
scans and my attempts to use gcut, and other skullstrip programs, has not
worked.
Thank you,
Michelle
On Fri, Dec 1, 2017 at 5:08 PM, Michelle VanTieghem
<[email protected]>
wrote:
Ok that worked. I sent the data for a subject with the skull stripping
issue
that is common in most of our dataset.
Thanks,
Michelle
On Fri, Dec 1, 2017 at 4:56 PM, Bruce Fischl <[email protected]> wrote:
try cd'ing to incoming not outgoing (the names are from our
perspective I think :)
On Fri, 1 Dec 2017, Michelle VanTieghem wrote:
yn-128-59-230-36:structural michellevantieghem2$ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use
of this site
220-shows implicit consent to our Acceptable Use Policy
outlined at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE: If, when doing a GET or PUT, you
encounter either
220-
220-229 Entering Extended Passive Mode
220-
220- and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220- try issuing the EPSV command prior
to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:michellevantieghem2):
anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/outgoing
250 Directory successfully changed.
ftp> put SB152_freesurfer.tar.gz
local: SB152_freesurfer.tar.gz remote:
SB152_freesurfer.tar.gz
229 Entering Extended Passive Mode (|||37860|).
553 Could not create file.
ftp> ls
229 Entering Extended Passive Mode (|||37896|).
150 Here comes the directory listing.
-rw-r--r-- 1 0 0 3812 Dec 01 06:10
README.1st
drwxrwsr-t 4 0 1046 4096 Nov 21 2014
flat
drwxrwsr-t 13 0 160 4096 Aug 19 2013
fsdev
drwxrwsr-t 14 0 1046 4096 Dec 05 2011
recon
drwxrwsr-t 3 0 18 4096 Jan 24 2005
sysadm
226 Directory send OK.
ftp> ls
229 Entering Extended Passive Mode (|||37892|).
150 Here comes the directory listing.
-rw-r--r-- 1 0 0 3812 Dec 01 06:10
README.1st
drwxrwsr-t 4 0 1046 4096 Nov 21 2014
flat
drwxrwsr-t 13 0 160 4096 Aug 19 2013
fsdev
drwxrwsr-t 14 0 1046 4096 Dec 05 2011
recon
drwxrwsr-t 3 0 18 4096 Jan 24 2005
sysadm
226 Directory send OK.
ftp> put SB152_freesurfer.tar.gz
local: SB152_freesurfer.tar.gz remote:
SB152_freesurfer.tar.gz
229 Entering Extended Passive Mode (|||37898|).
553 Could not create file.
ftp>
On Fri, Dec 1, 2017 at 4:50 PM, Bruce Fischl
<[email protected]> wrote:
can you paste the full session text into the email
(not as a screen shot)?
On Fri, 1 Dec 2017, Michelle VanTieghem wrote:
Hi, I am unsure whether this worked: see
attached screenshot.
Thanks!
M
On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl
<[email protected]> wrote:
yes, it should. You should just be able
to do a "put"
On Fri, 1 Dec 2017, Michelle VanTieghem
wrote:
Hi,
I am confused by the instructions
for the ftp. Once I am logged into the ftp and have
navigated to
the transfer/incoming
directory, how am I supposed to
find / access the file that I would ike to send
through? Does
terminal still recognize my
working directory before I logged
into the ftp?
Thanks!
Michelle
On Sat, Nov 18, 2017 at 2:54 PM,
Bruce Fischl <[email protected]> wrote:
Hi Michelle
probably best to tar and
gzip the entire subject directory and ftp it to us:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers
Bruce
On Sat, 18 Nov 2017,
Michelle VanTieghem wrote:
Hi,
Yes I can send you the
data - should I just attach the mprage file in the
email, or is
there
another
way to share the data
with freesurfer? Also, should I send one scan or
multiple
scans?
Thanks,
Michelle
On Sat, Nov 18, 2017
at 10:37 AM, Bruce Fischl
<[email protected]> wrote:
Hi Michelle
are you doing
anything out of the ordinary? Do you want to send us a
dataset and
we will
take a look? I
don't think 6.0 is very different from 5.3 in regard
to skull
stripping,
although it is
probably a bit better
Bruce
On Fri, 17 Nov
2017, Michelle VanTieghem wrote:
Hello,
I have
posted several times about problems with
skull-stripping with our
dataset.
We have tried gcut
and
multiple other options in other packages (AFNI, FSL, ANTS)
to remove
skull from
structural
images in
our dataset with little success.
Recently,
a colleague suggested this may be due to versions:
that 6.0
deals
with skull
stripping
much
better than 5.3.
I wanted
to ask if indeed this could be the case before I go
install 6.0
and re-run
everything in
my study.
Thank
you,
Michelle
--
Michelle
VanTieghem
PhD
student in Psychology
Developmental Affective Neuroscience Lab
Columbia
University
[email protected]
The information in
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--
Michelle VanTieghem
PhD student in
Psychology
Developmental
Affective Neuroscience Lab
Columbia University
[email protected]
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective
Neuroscience Lab
Columbia University
[email protected]
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
[email protected]
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
[email protected]
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
[email protected]
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
[email protected]
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
[email protected]
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
[email protected]
