The problem is that your original TLR108.bvec file is still in 3 rows, not 3 columns. You need to transpose the rows into columns.
Yes, there's an example config file that comes with the 5.3 distribution and it's as usual in $FREESURFER_HOME/bin/dmrirc.example. It's also described on the wiki, where all the info reflects the latest version of the software. http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
Please include freesurfer@nmr.mgh.harvard.edu in these emails so that the full thread is archived.
Thanks! a.y
On Tue, 12 Nov 2013, Laura Christine Anderson wrote:
Attached are bvecs and bvals files from dmri directory. Thanks for the advice on Freesurfer 5.3- is there a sample config file for Tracula for that version?
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
On 11/12/13 11:52 AM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Thanks. What do these files look like? /export/data/brain1/RSTOM/TLR108/dmri/bvecs /export/data/brain1/RSTOM/TLR108/dmri/bvals
These are the ones that the error message in trac-all.log is about, so something probably goes wrong with the conversion from your original files.
Also, I recommend very strongly that you use the latest version of tracula (from freesurfer 5.3). It's improved on both speed and performance.
On Tue, 12 Nov 2013, Laura Christine Anderson wrote:
Hi Anastasia, I have version 5.1. Attached are bvecs and bvals files with 3 and 1 columns respectively as well as the trac-all.log file.
Thanks! Laura
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
On 11/11/13 9:00 PM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Hi Laura - First of all, which version of freesurfer do you have? It looks to me like you've based your config file on the old example file that came with version 5.1.
Second, could you please convert your bvecs and bvals files to 3 columns and 1 column, respectively, then run trac-all and send the trac-all.log file that shows the errors that you get?
Thanks! a.y
On Mon, 11 Nov 2013, Laura Christine Anderson wrote:
Hi Anastasia, I am still struggling with this same error message, despite having rearranged the bval and bvec files in many different configurations (and making sure that each value in these files had the same number of digits, which I am not sure even matters). I am attaching my most recent bval and bvec files as well as the config file to see if you have any advice.
Thanks so much for your help!
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
On 10/15/13 11:17 AM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Hi Laura - This means that there is only 1 line in each of the files, so the end-of-line characters aren't recognized. I'd make sure that the file is saved as plain text.
a.y
On Tue, 15 Oct 2013, Laura Christine Anderson wrote:
> When I run "wc -l" on the bvec and bval files, I get "1" for both. > Running > just "wc" gives "1 279 3312" for bvec and "1 93 456" for bval > > Laura C. Anderson, B.A. > Graduate Student > Clinical & Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > > > > > On 10/14/13 5:18 PM, "Anastasia Yendiki" > ayendiki@nmr.mgh.harvard.edu > wrote: > >> >> Hi Laura - I don't think the error "bvecs and bvals don't have the >> same >> number of entries" should have to do with interspersed zero >> b-values. >> When >> you run "wc -l" on the bvecs and bvals files, what do you get? >> >> a.y >> >> On Mon, 14 Oct 2013, Laura Christine Anderson wrote: >> >>> Hi Anastasia, the bval/bvec files were created on a Mac and not >>> with >>> excel. I am not seeing the ^M character when I view the files in >>> unix >>> with >>> the more command or in gedit perhaps when I sent you the files, >>> something >>> became corrupted? I am wondering if my issue has something to do >>> with >>> the >>> fact that there are 3 sets of 30 rows with a b0 image before each >>> of >>> the 3 >>> sets. In the examples I have seen, the b0 images all seem to be at >>> the >>> beginning of the bvec and bval files. I am attaching a screenshot >>> of >>> the >>> bvec and bval files as I see them in case that is helpful. If you >>> would >>> rather me send the actual files again, what is the best way to do >>> that >>> without the formatting getting messed up? Before, I was using a >>> free >>> fileshare program. >>> >>> Thank you! >>> Laura >>> >>> Laura C. Anderson, B.A. >>> Graduate Student >>> Clinical & Developmental Psychology >>> University of Maryland >>> College Park, MD 20742 >>> BPS 0112 >>> >>> >>> >>> >>> On 10/11/13 2:38 PM, "Anastasia Yendiki" >>> ayendiki@nmr.mgh.harvard.edu >>> wrote: >>> >>>> >>>> Hi Laura - Were these bval/bvec files created on windows or with >>>> excel >>>> by >>>> any chance? When you view them in unix (with the more command for >>>> example) >>>> you'll see an "^M" character instead of every end-of-line. Can >>>> you >>>> try >>>> editing these files in a unix editor to fix that? Let me know if >>>> this >>>> solves the problem. >>>> >>>> a.y >>>> >>>> On Fri, 11 Oct 2013, Laura Christine Anderson wrote: >>>> >>>>> Hi Anastasia, >>>>> Thanks so much for your help! Attached are bvec, bval and >>>>> trac-all.log >>>>> files. >>>>> >>>>> I have been stuck at one of the preprocessing steps (trac all) >>>>> for >>>>> some >>>>> time and keep getting the >>>>> error: bvecs and bvals don't have the same number of entries. I >>>>> saw >>>>> a >>>>> couple blogs online about >>>>> this, but did not see any resolution. I am wondering if it is >>>>> because >>>>> the B0 images are >>>>> interspersed? (see attached bvec file). If you have any >>>>> insight, I >>>>> would love some feedback >>>>> whenever you get the chance. >>>>> >>>>> Laura >>>>> >>>>> >>>> >>>> >>>> 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. >>> >>> > > > >
Thanks! What do you mean by my "original TLR108.bvec file"? I think the issue may be that the bvec and bval files were originally created using dcm2nii before we had decided to use Tracula. I am just having trouble determining in which directory the original bvec and bval files were created, because it seems like those are outdated and incorrect and are affecting the creation of bvecs and bvals in the dmri directory
Sorry for my naïve questions- I really appreciate your help.
Laura
No problem. By original I mean the file that you specify by "set bvecfile = ..." in your config file. That one need to be in columns, not rows.
On Wed, 13 Nov 2013, Laura Christine Anderson wrote:
Thanks! What do you mean by my "original TLR108.bvec file"? I think the issue may be that the bvec and bval files were originally created using dcm2nii before we had decided to use Tracula. I am just having trouble determining in which directory the original bvec and bval files were created, because it seems like those are outdated and incorrect and are affecting the creation of bvecs and bvals in the dmri directory
Sorry for my naïve questions- I really appreciate your help.
Laura
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Laura Christine Anderson