We've generally seen better results with BBR, which is why it became the default setting.
On Thu, 6 Feb 2014, Jon Wieser wrote:
HI Anastasia,
I ran it again with the flirt registration and it finished ok. We did not have a specific reason for running it both ways. we are using the default setting for the dmrirc file. do you recommend one method over the other?
thanks again Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 3:07:12 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
That's entirely up to you, and whether you had a specific reason for running it both ways.
If you want to fix the bbr registration manually, check the trac-all.log file for a command at the end of bbregister, where it says "To check results, run".
On Thu, 6 Feb 2014, Jon Wieser wrote:
Hi Anastasia, We used both flirt and bbr registration in the dmrirc file, the Aparc+seg I just showedd you was from the BBR resitration. I looked at the flirt registration. it looks OK. should I rerun tracula using only the flirt registration? Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 11:00:25 AM Subject: Re: [Freesurfer] Fwd: trac-all -path error
So there's your culprit. You need to fix the intra-subject (diffusion-to-T1) registration. Did you use flirt or bbregister for that?
On Thu, 6 Feb 2014, Jon Wieser wrote:
Hi Anastasia, I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz the alignemenst is way off (in freeview, in the coronal view, the aparc+seg is rotated 45 degrees anti-clockwise), and parts of the FA map in the L ILF area are missing. the original DTI is not missing data in these areas. I have attached screenshots Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, February 5, 2014 6:35:12 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
Hi Jon - You need to look at the aparc+aseg after it has been mapped to diffusion space. It's possible that it looks fine in its original space but then maybe something goes wrong with the registration. So you should look at the aparc+aseg and aparc+aseg_mask files from the tracula dlabel/diff directory. These are in diffusion space and you can overlay them on the FA map to see if there's anything strange in the ILF area.
Hope this helps, a.y
On Tue, 14 Jan 2014, Jon Wieser wrote:
Hi anastasia I looked at the brainmask and the aparc+aseg. I did see anything missing in the area of the left ILF. I have attached the files. can you take a look at them? Thanks JOn
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, January 10, 2014 6:15:23 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? Anything missing there that might affect the left ILF?
a.y
On Wed, 8 Jan 2014, Jon Wieser wrote:
Dear freesurfer experts I'm getting the following error when runing trac-all -c dmrirc_single_subject -path
Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt Processing pathway 3 of 18... Initializing MCMC Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
I have attached the trac-all.log and trac-all.error files
I am running tracula 5.3
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 Anastasia, thanks for the information.we are able to process the DTI data successfully. we had 24 subjects which crashed during either the -perp or -path stage. I viewed the alignments between the FA and the alignement segmentations (flirt and bbr alignments), which ever alignment is better. I modify the dmrirc file to use that alignment and rerun trac-all , starting at the -prep stage all but 2 were successfuly processed with my method, that the dti tracts look good in freeview i didn't realign the registration using tkregister, because the anatomies are poor and lo res, making this realignment difficult thanks again!
JOn
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 3:16:16 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
We've generally seen better results with BBR, which is why it became the default setting.
On Thu, 6 Feb 2014, Jon Wieser wrote:
HI Anastasia,
I ran it again with the flirt registration and it finished ok. We did not have a specific reason for running it both ways. we are using the default setting for the dmrirc file. do you recommend one method over the other?
thanks again Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 3:07:12 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
That's entirely up to you, and whether you had a specific reason for running it both ways.
If you want to fix the bbr registration manually, check the trac-all.log file for a command at the end of bbregister, where it says "To check results, run".
On Thu, 6 Feb 2014, Jon Wieser wrote:
Hi Anastasia, We used both flirt and bbr registration in the dmrirc file, the Aparc+seg I just showedd you was from the BBR resitration. I looked at the flirt registration. it looks OK. should I rerun tracula using only the flirt registration? Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 11:00:25 AM Subject: Re: [Freesurfer] Fwd: trac-all -path error
So there's your culprit. You need to fix the intra-subject (diffusion-to-T1) registration. Did you use flirt or bbregister for that?
On Thu, 6 Feb 2014, Jon Wieser wrote:
Hi Anastasia, I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz the alignemenst is way off (in freeview, in the coronal view, the aparc+seg is rotated 45 degrees anti-clockwise), and parts of the FA map in the L ILF area are missing. the original DTI is not missing data in these areas. I have attached screenshots Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, February 5, 2014 6:35:12 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
Hi Jon - You need to look at the aparc+aseg after it has been mapped to diffusion space. It's possible that it looks fine in its original space but then maybe something goes wrong with the registration. So you should look at the aparc+aseg and aparc+aseg_mask files from the tracula dlabel/diff directory. These are in diffusion space and you can overlay them on the FA map to see if there's anything strange in the ILF area.
Hope this helps, a.y
On Tue, 14 Jan 2014, Jon Wieser wrote:
Hi anastasia I looked at the brainmask and the aparc+aseg. I did see anything missing in the area of the left ILF. I have attached the files. can you take a look at them? Thanks JOn
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, January 10, 2014 6:15:23 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? Anything missing there that might affect the left ILF?
a.y
On Wed, 8 Jan 2014, Jon Wieser wrote:
Dear freesurfer experts I'm getting the following error when runing trac-all -c dmrirc_single_subject -path
Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt Processing pathway 3 of 18... Initializing MCMC Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
I have attached the trac-all.log and trac-all.error files
I am running tracula 5.3
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 Jon - Glad to hear you could get around the registration issue. If the anatomical images are poor, then it makes sense that you'd encounter issues with bbregister, as bbregister relies on the surfaces that are derived exactly from those anatomical images.
Best, a.y
On Mon, 10 Feb 2014, Jon Wieser wrote:
Hi Anastasia, thanks for the information.we are able to process the DTI data successfully. we had 24 subjects which crashed during either the -perp or -path stage. I viewed the alignments between the FA and the alignement segmentations (flirt and bbr alignments), which ever alignment is better. I modify the dmrirc file to use that alignment and rerun trac-all , starting at the -prep stage all but 2 were successfuly processed with my method, that the dti tracts look good in freeview i didn't realign the registration using tkregister, because the anatomies are poor and lo res, making this realignment difficult thanks again!
JOn
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 3:16:16 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
We've generally seen better results with BBR, which is why it became the default setting.
On Thu, 6 Feb 2014, Jon Wieser wrote:
HI Anastasia,
I ran it again with the flirt registration and it finished ok. We did not have a specific reason for running it both ways. we are using the default setting for the dmrirc file. do you recommend one method over the other?
thanks again Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 3:07:12 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
That's entirely up to you, and whether you had a specific reason for running it both ways.
If you want to fix the bbr registration manually, check the trac-all.log file for a command at the end of bbregister, where it says "To check results, run".
On Thu, 6 Feb 2014, Jon Wieser wrote:
Hi Anastasia, We used both flirt and bbr registration in the dmrirc file, the Aparc+seg I just showedd you was from the BBR resitration. I looked at the flirt registration. it looks OK. should I rerun tracula using only the flirt registration? Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 11:00:25 AM Subject: Re: [Freesurfer] Fwd: trac-all -path error
So there's your culprit. You need to fix the intra-subject (diffusion-to-T1) registration. Did you use flirt or bbregister for that?
On Thu, 6 Feb 2014, Jon Wieser wrote:
Hi Anastasia, I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz the alignemenst is way off (in freeview, in the coronal view, the aparc+seg is rotated 45 degrees anti-clockwise), and parts of the FA map in the L ILF area are missing. the original DTI is not missing data in these areas. I have attached screenshots Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, February 5, 2014 6:35:12 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
Hi Jon - You need to look at the aparc+aseg after it has been mapped to diffusion space. It's possible that it looks fine in its original space but then maybe something goes wrong with the registration. So you should look at the aparc+aseg and aparc+aseg_mask files from the tracula dlabel/diff directory. These are in diffusion space and you can overlay them on the FA map to see if there's anything strange in the ILF area.
Hope this helps, a.y
On Tue, 14 Jan 2014, Jon Wieser wrote:
Hi anastasia I looked at the brainmask and the aparc+aseg. I did see anything missing in the area of the left ILF. I have attached the files. can you take a look at them? Thanks JOn
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, January 10, 2014 6:15:23 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error
Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? Anything missing there that might affect the left ILF?
a.y
On Wed, 8 Jan 2014, Jon Wieser wrote:
Dear freesurfer experts I'm getting the following error when runing trac-all -c dmrirc_single_subject -path
Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt Processing pathway 3 of 18... Initializing MCMC Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
I have attached the trac-all.log and trac-all.error files
I am running tracula 5.3
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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Jon Wieser