Hi Everyone --
I've been having difficulty getting Tracula to run smoothly on our cluster. Similar to others on the listserv, the bedpost step was not creating the necessary files causing an error during the -path step. Based on previous posts, I ran bedpostx on the dmri directory. This initially seemed to work (I no longer received the message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file.
Any help would be greatly appreciated.
Thanks,
Kiely
Hi Kiely - It's strange that bepostx would create ph2samples and not ph1samples. These are the orientation angles for the 2 anisotropic compartments, so if there's a 2nd there should be a 1st. Have you asked about it on the FSL list?
a.y
On Thu, 22 Dec 2011, Kiely Donnelly wrote:
Hi Everyone --
I've been having difficulty getting Tracula to run smoothly on our cluster. Similar to others on the listserv, the bedpost step was not creating the necessary files causing an error during the -path step. Based on previous posts, I ran bedpostx on the dmri directory. This initially seemed to work (I no longer received the message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file.
Any help would be greatly appreciated.
Thanks,
Kiely
Hi Anastasia,
Sorry for my slow reply. I am working with data that I only have access to intermittently. We were able to fix the problem by deleting the original files from the folder and re-running the bedpost step. The old files must have been interfering in some way.
I am hoping you can help me with a different problem I ran into. For several of our subjects, each pathway reconstruction fails and I get an error like the following for all 18 tracts:
Processing pathway 16 of 18... Initializing MCMC INFO: Path from initial control points is not entirely in mask INFO: or is self-intersecting INFO: Attemping to perturb control points ERROR: Path from initial control points is not entirely in mask ERROR: or is self-intersecting ERROR: Initialization failed ERROR: Pathway reconstruction failed Done in 0.216 sec.
I am able to view the FA image in native space, but when I attempt to view the FLIRT-registered FA image it's completely dark. Is there any reason you can think of that this may be happening?
Thanks in advance,
Kiely
On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Kiely - It's strange that bepostx would create ph2samples and not ph1samples. These are the orientation angles for the 2 anisotropic compartments, so if there's a 2nd there should be a 1st. Have you asked about it on the FSL list?
a.y
On Thu, 22 Dec 2011, Kiely Donnelly wrote:
Hi Everyone --
I've been having difficulty getting Tracula to run smoothly on our cluster. Similar to others on the listserv, the bedpost step was not creating the necessary files causing an error during the -path step. Based on previous posts, I ran bedpostx on the dmri directory. This initially seemed to work (I no longer received the message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file.
Any help would be greatly appreciated.
Thanks,
Kiely
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/**compliancelinehttp://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 Kiely,
I had a similar experience with one of my subjects, but I realized that the original diffusion image had a lot of signal loss in various regions and hence the subsequent registration steps failed.
It can happen when either intra-subject or inter-subject registration fails. I would inspect the original diffusion image (dmri/dwi_orig.nii.gz) and the original anatomical (dlabel/anat_brain_mask.nii.gz) to see if they have any problems (signal loss etc) which could lead to failures in registration as a first step.
If both your diffusion and anatomical are both good, then I'd try to do flirt seperately to see if you get the same results as the one produced by tracula.
Hope this is helpful,
Priti
Hi Anastasia,
Sorry for my slow reply. I am working with data that I only have access
to
intermittently. We were able to fix the problem by deleting the original
files from the folder and re-running the bedpost step. The old files must
have been interfering in some way.
I am hoping you can help me with a different problem I ran into. For
several of our subjects, each pathway reconstruction fails and I get an error like the following for all 18 tracts:
Processing pathway 16 of 18... Initializing MCMC INFO: Path from initial control points is not entirely in mask INFO: or is self-intersecting INFO: Attemping to perturb control points ERROR: Path from initial control points is not entirely in mask ERROR: or is self-intersecting ERROR: Initialization failed ERROR: Pathway reconstruction failed Done in 0.216 sec.
I am able to view the FA image in native space, but when I attempt to
view
the FLIRT-registered FA image it's completely dark. Is there any reason you can think of that this may be happening?
Thanks in advance,
Kiely
On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Kiely - It's strange that bepostx would create ph2samples and not
ph1samples. These are the orientation angles for the 2 anisotropic compartments, so if there's a 2nd there should be a 1st. Have you asked about it on the FSL list?
a.y On Thu, 22 Dec 2011, Kiely Donnelly wrote: Hi Everyone --
I've been having difficulty getting Tracula to run smoothly on our
cluster. Similar to others on the listserv, the bedpost step
was not creating the necessary files causing an error during the -path
step. Based on previous posts, I ran bedpostx on the dmri
directory. This initially seemed to work (I no longer received the
message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file.
Any help would be greatly appreciated. Thanks, Kiely
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/**compliancelinehttp://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.
-- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Priti,
Thanks for your help. I took another look at the original diffusion and anatomical images. The anatomical looks OK, but in the diffusion image a posterior region of the brain appears cutoff and when I view the image in freeview there is a green box in the lower left hand corner that I've never seen before (I've attached a shot). I'm new to Freesurfer so I would appreciate any help you may have.
Thanks again,
Kiely
On Tue, Jan 24, 2012 at 1:21 PM, Priti Srinivasan < rspriti@nmr.mgh.harvard.edu> wrote:
Hi Kiely,
I had a similar experience with one of my subjects, but I realized that the original diffusion image had a lot of signal loss in various regions and hence the subsequent registration steps failed.
It can happen when either intra-subject or inter-subject registration fails. I would inspect the original diffusion image (dmri/dwi_orig.nii.gz) and the original anatomical (dlabel/anat_brain_mask.nii.gz) to see if they have any problems (signal loss etc) which could lead to failures in registration as a first step.
If both your diffusion and anatomical are both good, then I'd try to do flirt seperately to see if you get the same results as the one produced by tracula.
Hope this is helpful,
Priti
Hi Anastasia,
Sorry for my slow reply. I am working with data that I only have access
to
intermittently. We were able to fix the problem by deleting the original
files from the folder and re-running the bedpost step. The old files must
have been interfering in some way.
I am hoping you can help me with a different problem I ran into. For
several of our subjects, each pathway reconstruction fails and I get an error like the following for all 18 tracts:
Processing pathway 16 of 18... Initializing MCMC INFO: Path from initial control points is not entirely in mask INFO: or is self-intersecting INFO: Attemping to perturb control points ERROR: Path from initial control points is not entirely in mask ERROR: or is self-intersecting ERROR: Initialization failed ERROR: Pathway reconstruction failed Done in 0.216 sec.
I am able to view the FA image in native space, but when I attempt to
view
the FLIRT-registered FA image it's completely dark. Is there any reason
you
can think of that this may be happening?
Thanks in advance,
Kiely
On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Kiely - It's strange that bepostx would create ph2samples and not
ph1samples. These are the orientation angles for the 2 anisotropic compartments, so if there's a 2nd there should be a 1st. Have you asked about it on the FSL list?
a.y On Thu, 22 Dec 2011, Kiely Donnelly wrote: Hi Everyone --
I've been having difficulty getting Tracula to run smoothly on our
cluster. Similar to others on the listserv, the bedpost step
was not creating the necessary files causing an error during the -path
step. Based on previous posts, I ran bedpostx on the dmri
directory. This initially seemed to work (I no longer received the
message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file.
Any help would be greatly appreciated. Thanks, Kiely
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline%3E. 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.
-- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Kiely - If part of the brain is cut off in dwi_orig.nii.gz, it means it was cut off in your original dicom. If there's actualy part of the brain missing in all the volumes in your diffusion series, you may not be able to reconstruct tracts that go through that part.
a.y
On Fri, 10 Feb 2012, Kiely Donnelly wrote:
Hi Priti, Thanks for your help. I took another look at the original diffusion and anatomical images. The anatomical looks OK, but in the diffusion image a posterior region of the brain appears cutoff and when I view the image in freeview there is a green box in the lower left hand corner that I've never seen before (I've attached a shot). I'm new to Freesurfer so I would appreciate any help you may have.
Thanks again,
Kiely
On Tue, Jan 24, 2012 at 1:21 PM, Priti Srinivasan rspriti@nmr.mgh.harvard.edu wrote: Hi Kiely,
I had a similar experience with one of my subjects, but I realized that the original diffusion image had a lot of signal loss in various regions and hence the subsequent registration steps failed. It can happen when either intra-subject or inter-subject registration fails. I would inspect the original diffusion image (dmri/dwi_orig.nii.gz) and the original anatomical (dlabel/anat_brain_mask.nii.gz) to see if they have any problems (signal loss etc) which could lead to failures in registration as a first step. If both your diffusion and anatomical are both good, then I'd try to do flirt seperately to see if you get the same results as the one produced by tracula. Hope this is helpful, Priti > Hi Anastasia, > > Sorry for my slow reply. I am working with data that I only have access to > intermittently. We were able to fix the problem by deleting the original files from the folder and re-running the bedpost step. The old files must > have been interfering in some way. > > I am hoping you can help me with a different problem I ran into. For several of our subjects, each pathway reconstruction fails and I get an error like the following for all 18 tracts: > > Processing pathway 16 of 18... > Initializing MCMC > INFO: Path from initial control points is not entirely in mask > INFO: or is self-intersecting > INFO: Attemping to perturb control points > ERROR: Path from initial control points is not entirely in mask > ERROR: or is self-intersecting > ERROR: Initialization failed > ERROR: Pathway reconstruction failed > Done in 0.216 sec. > > I am able to view the FA image in native space, but when I attempt to view > the FLIRT-registered FA image it's completely dark. Is there any reason you > can think of that this may be happening? > > Thanks in advance, > > Kiely > > > On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki < > ayendiki@nmr.mgh.harvard.edu> wrote: > >> Hi Kiely - It's strange that bepostx would create ph2samples and not ph1samples. These are the orientation angles for the 2 anisotropic compartments, so if there's a 2nd there should be a 1st. Have you asked about it on the FSL list? >> a.y >> On Thu, 22 Dec 2011, Kiely Donnelly wrote: >> Hi Everyone -- >>> I've been having difficulty getting Tracula to run smoothly on our cluster. Similar to others on the listserv, the bedpost step >>> was not creating the necessary files causing an error during the -path step. Based on previous posts, I ran bedpostx on the dmri >>> directory. This initially seemed to work (I no longer received the message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file. >>> Any help would be greatly appreciated. >>> Thanks, >>> Kiely >> 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 athttp://www.partners.org/**complianceline<http://www.partners.org/compliance
line>. 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.
-- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Kiely Donnelly -
Priti Srinivasan