Dear Anastasia and Tracula users,
I succesfully ran the longitudinal Tracula procedure for one subject. However, when I visualized the tracts, they look a bit weird (not smooth). Even if I played with the threshold on freeview, I couldn't make them look nice as in the wiki page. I checked the registration and it looks accurate, so I am not sure what could be wrong. I am attaching the messy looking tracts for your reference.
Could you tell me if I should run again with reinit=1 for these tracts?
Thank you very much for your time. Best regards,
Hi Jacek - Yes, these definitely look all over the place! It would help to get a screenshot of your subject's FA map and some more info on the acquisition. For example, is there any head motion? What's the voxel size and the number of gradient directions?
Best,
a.y
On Sun, 14 Feb 2016, Jacek Manko wrote:
Dear Freesurfer experts,
I have also noticed something wrong with the tracts I reconctructed. There were no erroors during the processing, but when I visualized all tracts in Freeview according to your command "freeview -tv my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit odd to say the least. Please have a look at the attached image.
I have also notice abnormal volumes of these tracts in comparison to your elmo-subjects. For example the volume of left uncinate for your tutorial subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy seems to coincide with with what you can spot in my screen, because it was my first impression that these tracts are extremely large.
I run tracula with default commands as you stated in your tutorial, no major changes were made. If there is anything you could advise me, I will very grateful. Are these results ok or I should udertake some steps? If you perhaps need some additional information I will be pleased to provide you with that as well.
Cheers,
Jacek
Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):
Dear Anastasia and Tracula users,I succesfully ran the longitudinal Tracula procedure for one subject. However, when I visualized the tracts, they look a bit weird (not smooth). Even if I played with the threshold on freeview, I couldn't make them look nice as in the wiki page. I checked the registration and it looks accurate, so I am not sure what could be wrong. I am attaching the messy looking tracts for your reference. Could you tell me if I should run again with reinit=1 for these tracts? Thank you very much for your time. Best regards, -- D.
Hi Jacek - I looked at the data that you uploaded. The problem is that both the b-value table and the gradient table that you were using were assuming that the b=0 images were interspersed throughout your scan, when in fact based on your dicoms they are all in the begining of the scan. So the 10 entries of 0.000 need to be in the beginning of the b-value table, not one every 7th image. Same with the gradient table. The gradient table also had some flipped coordinates that would cause a different problem down the line.
I was able to get the right tables by using mri_convert from the development version of freesurfer. The 5.3 version doesn't have the capability to read these tables from the dicoms but the 6.0 version will. In the meantime you can download the dev version and use mri_convert from that version.
Best,
a.y
On Sun, 14 Feb 2016, Jacek Manko wrote:
Dear Freesurfer experts,
I have also noticed something wrong with the tracts I reconctructed. There were no erroors during the processing, but when I visualized all tracts in Freeview according to your command "freeview -tv my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit odd to say the least. Please have a look at the attached image.
I have also notice abnormal volumes of these tracts in comparison to your elmo-subjects. For example the volume of left uncinate for your tutorial subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy seems to coincide with with what you can spot in my screen, because it was my first impression that these tracts are extremely large.
I run tracula with default commands as you stated in your tutorial, no major changes were made. If there is anything you could advise me, I will very grateful. Are these results ok or I should udertake some steps? If you perhaps need some additional information I will be pleased to provide you with that as well.
Cheers,
Jacek
Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):
Dear Anastasia and Tracula users,I succesfully ran the longitudinal Tracula procedure for one subject. However, when I visualized the tracts, they look a bit weird (not smooth). Even if I played with the threshold on freeview, I couldn't make them look nice as in the wiki page. I checked the registration and it looks accurate, so I am not sure what could be wrong. I am attaching the messy looking tracts for your reference. Could you tell me if I should run again with reinit=1 for these tracts? Thank you very much for your time. Best regards, -- D.
Hi Deniz - That cingulum looks way more inferior than it should be. It's hard to tell without being able to see the coronal view. It would make sense to reinitialize a couple of the tracts if the rest of the tracts in the subject look fine, but if they're all shifted inferior then it's a more general problem like misregistration with respect to the MNI template.
Best,
a.y
On Wed, 10 Feb 2016, denizzgursel wrote:
Dear Anastasia and Tracula users,
I succesfully ran the longitudinal Tracula procedure for one subject. However, when I visualized the tracts, they look a bit weird (not smooth). Even if I played with the threshold on freeview, I couldn't make them look nice as in the wiki page. I checked the registration and it looks accurate, so I am not sure what could be wrong. I am attaching the messy looking tracts for your reference.
Could you tell me if I should run again with reinit=1 for these tracts?
Thank you very much for your time. Best regards,
-- D.
Dear Anastasia,
Thank you! Wouldn't you mind for example sending me these tables? As far as I am concerned I need only one table for all my subjects, so that would help me a lot. The issue with flipped coordinates in the gradient table is, as I mentioned before, due to the fact that I obtained these values from motion corrected nifti data (which I was futilely trying to preprocess as well). Anyway, I would like to get back to to you with that issue later on.
Best, Jacek
Dnia 7-03-2016 o godz. 17:58 Anastasia Yendiki napisał(a):
Hi Jacek - I looked at the data that you uploaded. The problem is that both the b-value table and the gradient table that you were using were assuming that the b=0 images were interspersed throughout your scan, when in fact based on your dicoms they are all in the begining of the scan. So the 10 entries of 0.000 need to be in the beginning of the b-value table, not one every 7th image. Same with the gradient table. The gradient table also had some flipped coordinates that would cause a different problem down the line.
I was able to get the right tables by using mri_convert from the development version of freesurfer. The 5.3 version doesn't have the capability to read these tables from the dicoms but the 6.0 version will. In the meantime you can download the dev version and use mri_convert from that version.
Best,
a.y
On Sun, 14 Feb 2016, Jacek Manko wrote:
Dear Freesurfer experts,
I have also noticed something wrong with the tracts I reconctructed.
There were no erroors during the processing, but when I visualized all tracts in
Freeview according to your command "freeview -tv
my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit odd to say the least. Please
have a look at the attached image.
I have also notice abnormal volumes of these tracts in comparison to
your elmo-subjects. For example the volume of left uncinate for your tutorial
subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy
seems to coincide with with what you can spot in my screen, because it was my
first impression that these tracts are extremely large.
I run tracula with default commands as you stated in your tutorial, no
major changes were made. If there is anything you could advise me, I will very
grateful. Are these results ok or I should udertake some steps? If you
perhaps need some additional information I will be pleased to provide you with
that as well.
Cheers,
Jacek
Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):
Dear Anastasia and Tracula users,I succesfully ran the longitudinal Tracula procedure for one subject.
However, when I visualized the tracts, they look a bit weird (not smooth).
Even if I played with the threshold on freeview, I couldn't make them
look nice as in the wiki page. I checked the registration and it looks
accurate, so I am not sure what could be wrong. I am attaching the messy
looking tracts for your reference.
Could you tell me if I should run again with reinit=1 for these tracts? Thank you very much for your time. Best regards, -- D.
Dear Anastasia,
Thank you very much. This time I attach motion-corrected NIFTI-data (plus bval and bvec tables) that I have been unsuccessfully trying to process with Tracula. I also attach log file with error message. I suspect there must be something wrong with the tables again, but I am clueless on what that might be.
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=3xql45jb18z
Is there anything you could advise me on? Thanks in advance.
Best, Jacek Manko
Dnia 7-03-2016 o godz. 21:17 Anastasia Yendiki napisał(a):
Hi Jacek - I'm attaching the files.
a.y
On Mon, 7 Mar 2016, Jacek Manko wrote:
Dear Anastasia,
Thank you! Wouldn't you mind for example sending me these tables? As far
as I am concerned I need only one table for all my subjects, so that would help me a lot. The issue with flipped coordinates in the gradient table is, as I mentioned before, due to the fact that I obtained these values from motion corrected nifti data (which I was futilely trying to preprocess as well). Anyway, I would like to get back to to you with that issue later on.
Best, Jacek
Dnia 7-03-2016 o godz. 17:58 Anastasia Yendiki napisał(a):
Hi Jacek - I looked at the data that you uploaded. The problem is that both the b-value table and the gradient table that you were using were assuming that the b=0 images were interspersed throughout your scan, when in fact based on your dicoms they are all in the begining of the scan. So the 10 entries of 0.000 need to be in the beginning of the b-value table, not one every 7th image. Same with the gradient table. The gradient table also had some flipped coordinates that would cause a different problem down the line.
I was able to get the right tables by using mri_convert from the development version of freesurfer. The 5.3 version doesn't have the capability to read these tables from the dicoms but the 6.0 version will. In the meantime you can download the dev version and use mri_convert from that version.
Best,
a.y
On Sun, 14 Feb 2016, Jacek Manko wrote:
Dear Freesurfer experts,
I have also noticed something wrong with the tracts I reconctructed.
There were no erroors during the processing, but when I visualized all tracts in
Freeview according to your command "freeview -tv
my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit odd to say the least. Please
have a look at the attached image.
I have also notice abnormal volumes of these tracts in comparison to
your elmo-subjects. For example the volume of left uncinate for your tutorial
subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy
seems to coincide with with what you can spot in my screen, because it was my
first impression that these tracts are extremely large.
I run tracula with default commands as you stated in your tutorial, no
major changes were made. If there is anything you could advise me, I will very
grateful. Are these results ok or I should udertake some steps? If you
perhaps need some additional information I will be pleased to provide you with
that as well.
Cheers,
Jacek
Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):
Dear Anastasia and Tracula users,I succesfully ran the longitudinal Tracula procedure for one subject.
However, when I visualized the tracts, they look a bit weird (not smooth).
Even if I played with the threshold on freeview, I couldn't make them
look nice as in the wiki page. I checked the registration and it looks
accurate, so I am not sure what could be wrong. I am attaching the messy
looking tracts for your reference.
Could you tell me if I should run again with reinit=1 for these tracts? Thank you very much for your time. Best regards, -- D.
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