Hi Anastasia, Thanks for your reply. Oh, of course, sorry I didn't realise I was looking at the bvecs after the rotation. Now it makes sense.
Best wishes, Colm. > On 16 May 2014, at 16:59, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > wrote: > > > Hi Colm - The final version used is bvecs. The eddy current correction step > registers each DWI to the first b=0 image, and the same transformation is > applied to the corresponding gradient vector. This is a standard procedure > when doing eddy current correction by registration. > > Hope this helps, > a.y > >> On Fri, 16 May 2014, McGinnity, Colm wrote: >> >> Hi Anastasia, >> >> Many thanks for your help. >> I did reply but don't see the email on the forum. >> >> I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit >> confused - I've created a 3-column bvecs format file (I had been using for >> version 5.2.0). >> >> After running several I've noticed the 'bvecs' file in the dmri folder is >> slightly different from the input file, whereas the 'bvecs.norot' file >> matches the input file extactly. >> >> For example: >> File 2: >> 0.9200842 0.3251221 0.2185593 >> File 2: >> 0.919 0.3311 0.2141 >> >> Can you please clarify which is used, and if these differences can be >> ignored? >> >> Thanks and best wishes, >> Colm. >> >> >> -----Original Message----- >> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] >> Sent: 11 March 2014 00:39 >> To: McGinnity, Colm >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0 >> >> >> Hi Colm - Note that the information in the tutorial (particularly the part >> where gradient tables can be formatted in 3 rows or 3 columns) pertains to >> the latest tracula update: >> http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates >> >> You're using an older version that only supports the 3-column format. I have >> no idea if this is what's causing the error without looking at your >> trac-all.log, but this would be a first guess. >> >> a.y >> >>> On Mon, 10 Mar 2014, McGinnity, Colm wrote: >>> >>> Dear Experts, >>> >>> I am very new to TRACULA, I apologise for what is probably a silly question. >>> >>> I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0): >>> >>> awk: cmd. line:1: fatal: cannot open file `0' for reading (No such >>> file or >>> directory) >>> mri_concat --i >>> /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz >>> --mean --o /home/k1193186/ >>> FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz >>> niiRead(): error opening file /home/k1193186/ >>> FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz >>> ninputs = 1 >>> Checking inputs >>> ERROR: reading >>> /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz >>> >>> Can anyone tell me what this means and how to fix this, please? >>> I’m guessing I’ve set up my configuration wrong or have the files in >>> the wrong place? >>> >>> Many thanks! >>> Best wishes, >>> Colm. >>> King's College London >> >> >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
