Hi Vincent - If you upload the tracula dirs for this particular time point, I'll take a look.
a.y
On Mon, 20 May 2013, Vincent Brunsch wrote:
Hi Anastasia, Thanks for your help! I had this issue with 4 tracts in total. I just want to add that before rerunning dmri_pathstats not only pathstats.overall but also pathstats.byvoxel was affected (in the latter there were no matrix entries at all). I found some information in the trac-all.log but not explicitly the command line <- this was found in pathstats.overall.txt, though.
After rerunning dmri_pathstats everything looks great now for 3 out of the 4 tracts, YEAH! I am not sure what to do with the last one, though: Here, the same error occurs but in cpts.map.txt no two lines are identical:
For lh.cst: 58 48 10 62 51 21 65 55 26 70 58 35 72 57 39 64 55 56
Would you suggest deleting randomly one time point for this tract of this subject? Thanks! Vincent
Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki:
Hi Vincent - Thanks for bringing this to my attention. I can see what might cause this glitch (only in the longitudinal case) and I'll fix it in the next version.
In the meantime, if you delete one of the two identical lines from cpts.map.txt, and then rerun the dmri_pathstats command line that you'll find in the trac-all.log of your subject, it should regenerate the stats files correctly. Sorry for the inconvenience.
a.y
On Fri, 17 May 2013, vbrunsch@nmr.mgh.harvard.edu wrote:
Dear Anastasia,
When running the longitudinal tracula version on our 39 subjects I found for some of them "nan"-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the control points of this path, two of them are the same. Do you know how this could have happened / what to do?
E.g. control points of forceps major from a subject (cpts.map.txt), see 4th and 5th control point:
63 20 39 67 31 39 59 43 38 52 42 38 52 42 38 43 32 38 50 19 33
And the respective pathstats.overall.txt: Count 1500 Volume 370 Len_Min 62 Len_Max 99 Len_Avg 78.9307 Len_Center 0 AD_Avg 0.00155598 AD_Avg_Weight 0.00158424 AD_Avg_Center -nan RD_Avg 0.000438439 RD_Avg_Weight 0.000401328 RD_Avg_Center -nan MD_Avg 0.000810952 MD_Avg_Weight 0.000795633 MD_Avg_Center -nan FA_Avg 0.662419 FA_Avg_Weight 0.696257 FA_Avg_Center -nan
Thanks for your help!! :) Best, Vincent
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Anastasia, the files are here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/TC055FB.v2/dpathlong/lh.cst_AS_avg33_mni_bbr
The base is here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/longbaseTC055FB
Freesurfer outputs: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/freesurfer/subjects/TC055FB.v2 and /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/freesurfer/subjects/TC055FB.v2.long.longbaseTC055FB
You should have permissions to see everything, if not, please tell me.
Fyi: Maybe it's random, but the 4 errors occurred all in the first time point.
Thanks, Vincent
Hi Vincent - If you upload the tracula dirs for this particular time point, I'll take a look.
a.y
On Mon, 20 May 2013, Vincent Brunsch wrote:
Hi Anastasia, Thanks for your help! I had this issue with 4 tracts in total. I just want to add that before rerunning dmri_pathstats not only pathstats.overall but also pathstats.byvoxel was affected (in the latter there were no matrix entries at all). I found some information in the trac-all.log but not explicitly the command line <- this was found in pathstats.overall.txt, though.
After rerunning dmri_pathstats everything looks great now for 3 out of the 4 tracts, YEAH! I am not sure what to do with the last one, though: Here, the same error occurs but in cpts.map.txt no two lines are identical:
For lh.cst: 58 48 10 62 51 21 65 55 26 70 58 35 72 57 39 64 55 56
Would you suggest deleting randomly one time point for this tract of this subject? Thanks! Vincent
Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki:
Hi Vincent - Thanks for bringing this to my attention. I can see what might cause this glitch (only in the longitudinal case) and I'll fix it in the next version.
In the meantime, if you delete one of the two identical lines from cpts.map.txt, and then rerun the dmri_pathstats command line that you'll find in the trac-all.log of your subject, it should regenerate the stats files correctly. Sorry for the inconvenience.
a.y
On Fri, 17 May 2013, vbrunsch@nmr.mgh.harvard.edu wrote:
Dear Anastasia,
When running the longitudinal tracula version on our 39 subjects I found for some of them "nan"-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the control points of this path, two of them are the same. Do you know how this could have happened / what to do?
E.g. control points of forceps major from a subject (cpts.map.txt), see 4th and 5th control point:
63 20 39 67 31 39 59 43 38 52 42 38 52 42 38 43 32 38 50 19 33
And the respective pathstats.overall.txt: Count 1500 Volume 370 Len_Min 62 Len_Max 99 Len_Avg 78.9307 Len_Center 0 AD_Avg 0.00155598 AD_Avg_Weight 0.00158424 AD_Avg_Center -nan RD_Avg 0.000438439 RD_Avg_Weight 0.000401328 RD_Avg_Center -nan MD_Avg 0.000810952 MD_Avg_Weight 0.000795633 MD_Avg_Center -nan FA_Avg 0.662419 FA_Avg_Weight 0.696257 FA_Avg_Center -nan
Thanks for your help!! :) Best, Vincent
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
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
vbrunsch＠nmr.mgh.harvard.edu