All,
Just curious about the current estimated timeline for version 5.1, trying to schedule some projects around it. Thanks!
-Derin
Hi Derin,
since I gave the initial estimate of end of last year, I feel I should answer. At that point we planed to include only the new longitudinal stream. The new longitudinal stream with single voxel space has been tested and is included since early November.
However with this release we have started to include new and more rigorous tests (including test-retest data) and in addition are lucky to have several people manually inspect results. Consequently, we discovered several minor problems in the cross sectional stream (these are some special cases where something goes wrong, e.g. skull stripping, surfaces etc). Some fixes lead to other issues etc. We are currently testing at least the 3rd release candidate.
I am not the right person to give another estimate as all this is related to the standard cross sectional freesurfer stream.
Best, Martin
On Thu, 2011-01-20 at 10:40 -0600, Derin Cobia wrote:
All,
Just curious about the current estimated timeline for version 5.1, trying to schedule some projects around it. Thanks!
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Derin
we are tracking down some issues with it and hope to have it out within a month
cheers Bruce On Thu, 20 Jan 2011, Derin Cobia wrote:
All,
Just curious about the current estimated timeline for version 5.1, trying to schedule some projects around it. Thanks!
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, We have two studies being conducted (one cross-sectional and one longitudinal) Some of the subjects in have a lot of atrophy and have large ventircles.
For the cross-sectional analysis stream are there many differences between 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for cross-sectional analysis ?
(I understand that for the longitudinal study, I should wait for 5.1 and process all the timepoints with 5.1)
Thanks Mehul
On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Derin
we are tracking down some issues with it and hope to have it out within a month
cheers Bruce On Thu, 20 Jan 2011, Derin Cobia wrote:
All,
Just curious about the current estimated timeline for version 5.1, trying
to schedule some projects around it. Thanks!
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Mehul,
I think 5.1 will work better for large ventricles than 4.5, but I'll be interested to hear your experience.
cheers Bruce On Tue, 15 Feb 2011, Mehul Sampat wrote:
Hi Bruce, We have two studies being conducted (one cross-sectional and one longitudinal) Some of the subjects in have a lot of atrophy and have large ventircles.
For the cross-sectional analysis stream are there many differences between 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for cross-sectional analysis ?
(I understand that for the longitudinal study, I should wait for 5.1 and process all the timepoints with 5.1)
Thanks Mehul
On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Derin
we are tracking down some issues with it and hope to have it out within a month
cheers Bruce On Thu, 20 Jan 2011, Derin Cobia wrote:
All,
Just curious about the current estimated timeline for version 5.1, trying
to schedule some projects around it. Thanks!
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Bruce,
Okay. I will try it out 5.1 in the future and compare it to 4.5.
I also have a question about comparisons between version 4.5 and 5.0
In some cases, I saw that FS 4.5 does a slightly better job at skull stripping than FS 5.0. Esentially, FS 5.0 seems to make errors in the back of the brain and cuts out some tissue. (Please see attached images).
The images are the same slice from the same subject processed with FS 4.5 and 5.0 (This happens across 5-10 slices) In 5.0, I used the following command: recon-all -s "subj--id" -i "nifti-file" -all -nuintensitycor-3T (I have seen this issue in atleast 5 subjects in our data)
Since 5.0 uses the graph cuts, could the error be due the combination of (graph cuts + -nuintensitycor-3T) ? Also, I guess I could run 5.0 and use only graph cuts or -nuintensitycor-3T to isolate the error ?
Thanks Mehul
On Tue, Feb 15, 2011 at 12:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Mehul,
I think 5.1 will work better for large ventricles than 4.5, but I'll be interested to hear your experience.
cheers Bruce
On Tue, 15 Feb 2011, Mehul Sampat wrote:
Hi Bruce,
We have two studies being conducted (one cross-sectional and one longitudinal) Some of the subjects in have a lot of atrophy and have large ventircles.
For the cross-sectional analysis stream are there many differences between 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for cross-sectional analysis ?
(I understand that for the longitudinal study, I should wait for 5.1 and process all the timepoints with 5.1)
Thanks Mehul
On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Derin
we are tracking down some issues with it and hope to have it out within a month
cheers Bruce On Thu, 20 Jan 2011, Derin Cobia wrote:
All,
Just curious about the current estimated timeline for version 5.1, trying
to schedule some projects around it. Thanks!
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi,
For what it's worth, I have seen a very similar skull-strip failure on at least one of my brains processed with Freesurfer 5.0 but not using the -nuintensitycor-3T flag. Happy to send data, if helpful.
Best. Michael
On Wed, Feb 16, 2011 at 2:03 PM, Mehul Sampat mpsampat@gmail.com wrote:
Hi Bruce,
Okay. I will try it out 5.1 in the future and compare it to 4.5.
I also have a question about comparisons between version 4.5 and 5.0
In some cases, I saw that FS 4.5 does a slightly better job at skull stripping than FS 5.0. Esentially, FS 5.0 seems to make errors in the back of the brain and cuts out some tissue. (Please see attached images).
The images are the same slice from the same subject processed with FS 4.5 and 5.0 (This happens across 5-10 slices) In 5.0, I used the following command: recon-all -s "subj--id" -i "nifti-file" -all -nuintensitycor-3T (I have seen this issue in atleast 5 subjects in our data)
Since 5.0 uses the graph cuts, could the error be due the combination of (graph cuts + -nuintensitycor-3T) ? Also, I guess I could run 5.0 and use only graph cuts or -nuintensitycor-3T to isolate the error ?
Thanks Mehul
On Tue, Feb 15, 2011 at 12:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mehul,
I think 5.1 will work better for large ventricles than 4.5, but I'll be interested to hear your experience.
cheers Bruce On Tue, 15 Feb 2011, Mehul Sampat wrote:
Hi Bruce, We have two studies being conducted (one cross-sectional and one longitudinal) Some of the subjects in have a lot of atrophy and have large ventircles.
For the cross-sectional analysis stream are there many differences between 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for cross-sectional analysis ?
(I understand that for the longitudinal study, I should wait for 5.1 and process all the timepoints with 5.1)
Thanks Mehul
On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Derin
we are tracking down some issues with it and hope to have it out within a month
cheers Bruce On Thu, 20 Jan 2011, Derin Cobia wrote:
All,
Just curious about the current estimated timeline for version 5.1, trying
to schedule some projects around it. Thanks!
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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.
you can try the -no-gcut flag at the end of recon-all to disable the gcut stage within skullstrip. for the next release (5.1), gcut is being made more conservative to reduce these failures.
n.
On Wed, 2011-02-16 at 14:30 -0500, Michael Waskom wrote:
Hi,
For what it's worth, I have seen a very similar skull-strip failure on at least one of my brains processed with Freesurfer 5.0 but not using the -nuintensitycor-3T flag. Happy to send data, if helpful.
Best. Michael
On Wed, Feb 16, 2011 at 2:03 PM, Mehul Sampat mpsampat@gmail.com wrote:
Hi Bruce,
Okay. I will try it out 5.1 in the future and compare it to 4.5.
I also have a question about comparisons between version 4.5 and 5.0
In some cases, I saw that FS 4.5 does a slightly better job at skull stripping than FS 5.0. Esentially, FS 5.0 seems to make errors in the back of the brain and cuts out some tissue. (Please see attached images).
The images are the same slice from the same subject processed with FS 4.5 and 5.0 (This happens across 5-10 slices) In 5.0, I used the following command: recon-all -s "subj--id" -i "nifti-file" -all -nuintensitycor-3T (I have seen this issue in atleast 5 subjects in our data)
Since 5.0 uses the graph cuts, could the error be due the combination of (graph cuts + -nuintensitycor-3T) ? Also, I guess I could run 5.0 and use only graph cuts or -nuintensitycor-3T to isolate the error ?
Thanks Mehul
On Tue, Feb 15, 2011 at 12:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mehul,
I think 5.1 will work better for large ventricles than 4.5, but I'll be interested to hear your experience.
cheers Bruce On Tue, 15 Feb 2011, Mehul Sampat wrote:
Hi Bruce, We have two studies being conducted (one cross-sectional and one longitudinal) Some of the subjects in have a lot of atrophy and have large ventircles.
For the cross-sectional analysis stream are there many differences between 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for cross-sectional analysis ?
(I understand that for the longitudinal study, I should wait for 5.1 and process all the timepoints with 5.1)
Thanks Mehul
On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Derin
we are tracking down some issues with it and hope to have it out within a month
cheers Bruce On Thu, 20 Jan 2011, Derin Cobia wrote:
All,
Just curious about the current estimated timeline for version 5.1, trying
to schedule some projects around it. Thanks!
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Derin Cobia -
Martin Reuter -
Mehul Sampat -
Michael Waskom -
Nick Schmansky