---------- Forwarded message ---------- From: "Salil Soman" <salso...@stanford.edu> Date: Jan 12, 2014 1:28 PM Subject: Re: problem with bvecs file with new (12/13) TRACULA code To: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> Cc:
Hi, > > Thank you for your email. Taking the .bval and bvec files outputed by > dcm2nii (which are row format) and transposing them to column format was > resulting in the blank rows that were causing troubles. Running this > command got rid of the problems and allowed trac-all prep / bedp / and path > to complete without errors: > > sed '/^\s*$/d' > > > Thanks, > > Sal > > > On Fri, Jan 10, 2014 at 3:57 PM, Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu> wrote: > >> >> Hi Sal - It looks like a problem with the spaces at the end of the lines >> of the bvecs file. If you remove those spaces, it should work. Thanks for >> bringing this to my attention - the row-formatted bvecs files are new in >> this version and I'll make sure to allow them to have spaces at the end of >> the lines in the future. >> >> a.y >> >> >> On Thu, 9 Jan 2014, Salil Soman wrote: >> >> Hi, >>> >>> I am re-running GE acquired 3T product DTI data which ran without >>> trouble through the older tracula code. >>> However, now when I run the code, the bvec file that gets generated has >>> an extra 0 placed at the very end, >>> and then trac-all -prep eventually fails because it complains the bvec >>> and bvals files have non-matching >>> number of entries. I do have the dorotbvecs option set to 1 (as I had >>> before). Any suggestions on what I am >>> doing incorrectly would be greatly appreciated. I have attached the bvec >>> and bval files I am providing a >>> input. >>> >>> Best wishes, >>> >>> Sal >>> -- >>> Salil Soman, MD, MS >>> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory >>> Fellow - Palo Alto War Related Illness and Injury Study Center >>> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care >>> System >>> >>> >>> >> >> 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. >> > > > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care > System >
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