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.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/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 <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 attached screenshot.

            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 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
            <fischl@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 
                                                mrv2115@columbia.edu




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            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
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                                    --
                                    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 



--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 



--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 



--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2115@columbia.edu