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 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Tue, 19 Dec 2017 15:25:14 -0800 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20171219
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.vantieghem@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.vantieghem@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.vantieghem@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 <fischl@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/compute r/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 < fischl@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 attachedscreenshot.
Thanks! M On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl <fischl@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 <fischl@nmr.mgh.harvard.edu> wrote: Hi Michelle
probably best to tar and gzip the entiresubject directory and ftp it to us:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce On Sat, 18 Nov 2017, Michelle VanTieghemwrote:
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 fischl@nmr.mgh.harvard.edu wrote: Hi Michelle
are you doing anything outof 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 severaltimes 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 colleaguesuggested this may be due to versions: that 6.0 deals with skull stripping much better than 5.3.
I wanted to ask ifindeed 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 inPsychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
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-- Michelle VanTieghem PhD student in Psychology Developmental AffectiveNeuroscience Lab Columbia University mrv2115@columbia.edu
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
