that's good to hear, thanks for letting us know Michelle BruceOn Mon, 22 Jan 2018, Michelle VanTieghem wrote:
Hi,
I went ahead and re-processed all of our data with the newest version (6.0)
of freesurfer (I didn't hear back from anyone on this issue for over a
month). It does make a significant difference for our dataset. Pial mater is
no longer labeled as gray matter with version 6, which was a significant
issue for the majority of our images when using version 5.3. I've attached
screen shot examples her (v5.3 on right, v6 on left). I thought this would
be useful for other users to know!
Thanks,
Michelle
On Tue, Jan 2, 2018 at 9:36 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Michelle
if you point me at a dataset (an entire subject dir gzipped and
uploaded to our ftp site) and some voxel coordinates of where
you see problems, I'll take a look.
cheers
Bruce
On Fri, 22 Dec 2017, Michelle VanTieghem wrote:
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
<michelle.vantieg...@gmail.com> 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
<michelle.vantieg...@gmail.com> 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
<michelle.vantieg...@gmail.com>
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
<fis...@nmr.mgh.harvard.edu> 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
<fis...@nmr.mgh.harvard.edu> 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
<fis...@nmr.mgh.harvard.edu> 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
<fis...@nmr.mgh.harvard.edu> 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
<fis...@nmr.mgh.harvard.edu>
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
mrv2...@columbia.edu
The
information in
this e-mail is intended only for the
person to whom it
is
addressed. If you
believe this e-mail was sent to you in
error and the
e-mail
contains patient
information, please contact the Partners
Compliance
HelpLine at
http://www.partners.org/complianceline .
If the e-mail was
sent to you in
error
but
does not contain
patient information, please contact the
sender and
properly
dispose of the e-mail.
--
Michelle VanTieghem
PhD
student in
Psychology
Developmental
Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle
VanTieghem
PhD student in
Psychology
Developmental
Affective
Neuroscience Lab
Columbia
University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective
Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
