Hi All,
Could you please help with the following:
When we run mris_anatomical_stats with FS 4.0.1 we can see the results on the terminal and we are able to get a log file, but this latter appears always blank.
Countrarywise, when we use mris_anatomical_stats with FS 3.0.5 on the same set of data we are able to get a log file with the outputs but we have noticed these two things:
1) results are not identical to the ones coming from mris_anatomical_stats with FS 4.0.1; in particular, we see minimal differences when looking at the average cortical thickness and major differences when looking at the three last measures (i.e. average integrated rectified mean curvature, average integrated rectified Gaussian curvature, folding index);
2) the results reported in the in the log file for the total surface area always the ones coming from the pial surface whatever surface name we specified (pial or white)
Thanks in advance for your help,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5C203B
Bethesda, MD, 20892 - USA
ph #: 001-301-496.7368
fax #: 001-301-402.0373
***********************
Antonio,
Can you send me a command-line that shows usage of creation of the log file? That is, where it should be created, but isnt.
In v3.0.5, the last three measures that you mention are wrong, and this problem was fixed in v4.0.0.
Does the v4.0 mris_anatomical_stats always produce results for the pial surface? I think that was broken in the v3.0.5 version as well.
Nick
On Tue, 2007-12-18 at 11:02 -0500, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi All,
Could you please help with the following:
When we run mris_anatomical_stats with FS 4.0.1 we can see the results on the terminal and we are able to get a log file, but this latter appears always blank.
Countrarywise, when we use mris_anatomical_stats with FS 3.0.5 on the same set of data we are able to get a log file with the outputs but we have noticed these two things:
results are not identical to the ones coming frommris_anatomical_stats with FS 4.0.1; in particular, we see minimal differences when looking at the average cortical thickness and major differences when looking at the three last measures (i.e. average integrated rectified mean curvature, average integrated rectified Gaussian curvature, folding index);
the results reported in the in the log file for the totalsurface area always the ones coming from the pial surface whatever surface name we specified (pial or white)
Thanks in advance for your help,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5C203B
Bethesda, MD, 20892 - USA
ph #: 001-301-496.7368
fax #: 001-301-402.0373
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick, This is what I wrote (FS 4.0.1): mris_anatomical_stats -log logfile -l ?h.cortex.label subjid ?h NB: the logfile is created but is empty.
Thanks,
Antonio
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, December 18, 2007 3:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] mris_anatomical_stats
Antonio,
Can you send me a command-line that shows usage of creation of the log file? That is, where it should be created, but isnt.
In v3.0.5, the last three measures that you mention are wrong, and this problem was fixed in v4.0.0.
Does the v4.0 mris_anatomical_stats always produce results for the pial surface? I think that was broken in the v3.0.5 version as well.
Nick
On Tue, 2007-12-18 at 11:02 -0500, Gallo, Antonio (NIH/NINDS) [F]
wrote:
Hi All,
Could you please help with the following:
When we run mris_anatomical_stats with FS 4.0.1 we can see the
results
on the terminal and we are able to get a log file, but this latter appears always blank.
Countrarywise, when we use mris_anatomical_stats with FS 3.0.5 on the same set of data we are able to get a log file with the outputs but
we
have noticed these two things:
results are not identical to the ones coming frommris_anatomical_stats with FS 4.0.1; in particular, we see minimal differences when looking at the average cortical thickness and major differences when looking at the three last measures (i.e. average integrated rectified mean curvature, average integrated rectified Gaussian curvature, folding index);
the results reported in the in the log file for the totalsurface area always the ones coming from the pial surface whatever surface name we specified (pial or white)
Thanks in advance for your help,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5C203B
Bethesda, MD, 20892 - USA
ph #: 001-301-496.7368
fax #: 001-301-402.0373
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Antonio,
There was a bug in mris_anatomical_state that was preventing the log file from being written. Which freesurfer OS dist do you use? I can post a fixed version of the binary.
Nick
On Tue, 2007-12-18 at 16:03 -0500, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi Nick, This is what I wrote (FS 4.0.1): mris_anatomical_stats -log logfile -l ?h.cortex.label subjid ?h NB: the logfile is created but is empty.
Thanks,
Antonio
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, December 18, 2007 3:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] mris_anatomical_stats
Antonio,
Can you send me a command-line that shows usage of creation of the log file? That is, where it should be created, but isnt.
In v3.0.5, the last three measures that you mention are wrong, and this problem was fixed in v4.0.0.
Does the v4.0 mris_anatomical_stats always produce results for the pial surface? I think that was broken in the v3.0.5 version as well.
Nick
On Tue, 2007-12-18 at 11:02 -0500, Gallo, Antonio (NIH/NINDS) [F]
wrote:
Hi All,
Could you please help with the following:
When we run mris_anatomical_stats with FS 4.0.1 we can see the
results
on the terminal and we are able to get a log file, but this latter appears always blank.
Countrarywise, when we use mris_anatomical_stats with FS 3.0.5 on the same set of data we are able to get a log file with the outputs but
we
have noticed these two things:
results are not identical to the ones coming frommris_anatomical_stats with FS 4.0.1; in particular, we see minimal differences when looking at the average cortical thickness and major differences when looking at the three last measures (i.e. average integrated rectified mean curvature, average integrated rectified Gaussian curvature, folding index);
the results reported in the in the log file for the totalsurface area always the ones coming from the pial surface whatever surface name we specified (pial or white)
Thanks in advance for your help,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5C203B
Bethesda, MD, 20892 - USA
ph #: 001-301-496.7368
fax #: 001-301-402.0373
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Gallo, Antonio (NIH/NINDS) [F] -
Nick Schmansky