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 fischl@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:
- 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.
- 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
- The aseg almost always labels the remaining skull as gray matter,
which then influences the icv and wbv measurements. W
- 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 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 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
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
that's good to hear, thanks for letting us know Michelle Bruce On 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 fischl@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.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 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 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 -- 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Michelle VanTieghem