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. > >>> > >>> > >>> > >>> > >>> > >>> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > 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.
trac-all.log
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
