Hi Barbara, I checked the path. The folder with the trac-all output is is the very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks
On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp <bakk....@googlemail.com> wrote: > Hi Michele, > > You would have to make sure that the files are written to the same folder > for both commands (recon-all and trac-all) > Right now it seems you wrote the output of recon-all to > /PHShome/my738/FSout/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b/ > > and trac-all output to > /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/ > > This is what the code was looking for but did not find: > Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz > > What path did you specify for the T1 segmentations (by recon-all) in your > configuration file? > > Hope it helps, > All the best, > Barbara > > > On 03.09.14 17:31, Michele Cavallari wrote: > > Hi Barbara, > thanks again for your help. > I checked the bvecs file using the 'more' command, and (as you pointed > out) there was some extra text. This was likely due to MS-excel formatting, > which I have used to reshape the bvecs file from row to column > configuration. Such extra text was not part of the original bvecs file > organized in rows though, but tracula was not giving errors as well. > So, take home message#1 > It is not true that FreeSurfer 5.3 allows both rows and columns > configuration of the bvecs (as stated in the wiki page). Or at least that's > not true for all the scanners. I'd recommend a column configuration of the > bvecs, even with FreeSurfer 5.3. > Also - take home message#2 > verify that there's no extra text due to excel formatting in the reshaped > bvecs file. > > That said, now this lead me to the next error! > It seems that there's a problem with the recon-all output that I'm using > (?). However, both the log file and the output of the recon-all processing > seem fine to me. > Here is the detail of the error message I am getting > ERROR: fio_pushd: path/to/dlabel/mni > And attached are the log files of both tracula pre-processing (with > errors) and recon-all (apparently without errors). > > Any help/suggestions? > Thanks. > > > > On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp <bakk....@googlemail.com > > wrote: > >> Hi Michele, >> >> This might be the solution - try the command 'more' in unix on your >> column bvec and bval, they should each have one (bval) and three (bvec) >> columns and no strange symbols. But you have these symbols in the bvec-file >> (probably because you have extra formatting information, that is not needed >> and an obstacle to Tracula). >> >> more original_columns.bval >> >> 0 >> >> 0 >> >> 0 >> >> 0 >> >> 0 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> 1000 >> >> NEURO-222:tracula_help NEURO-222$ more original_columns.bvec >> >> 0 0 0 >> >> 0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 >> 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 >> 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 >> ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 >> 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 >> -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 >> ^M-0.414 >> 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 >> 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 >> ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025 >> >> >> You are ending up with multiple columns in the second row, please make >> sure they are 3 columns. >> >> >> Good luck, >> >> Barbara >> >> >> On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp < >> bakk....@googlemail.com> wrote: >> >>> Hi Michele, >>> >>> Do you use the dicoms or the nifti files as input to TRACULA? >>> Also, I think the complete trac-all.log could be even more helpful. >>> I am a newbie myself but I am having a similar problem, so I am trying >>> to find a solution as well :). >>> >>> Best, >>> Barbara >>> >>> >>> On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari < >>> mic...@bwh.harvard.edu> wrote: >>> >>>> Hi Barbara, >>>> thanks for your reply. I checked the dwi series on a viewer and it looks >>>> fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions >>>> specified in the bval/bvec. Also, I was able to obtain the FA and MD >>>> maps >>>> through fsl using the very same dicoms and bval/bvec. >>>> Any suggestion? >>>> Thanks >>>> >>>> >>>> On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp >>>> <bakk....@googlemail.com> wrote: >>>> Dear Michele, >>>> >>>> I cannot find anything wrong with your bvec and bval files. >>>> Seeing as you had an errormessage related to the dwi (the one about the >>>> dwi_frame.nii.gz): Did you check that your dwi data have the same >>>> amount of >>>> volumes as entries in bvec and bval? >>>> >>>> Good luck, >>>> Barbara >>>> >>>> >>>> >>>> On 28/08/2014 22:47, Michele Cavallari wrote: >>>> Hi, >>>> I'm having some problems with the first command of the tracula pipeline. >>>> I am using FreeSurfer 5.3 on a mac (OS 10.9). >>>> The problem seems to be related to the bvecs file. I received the >>>> following >>>> error message: >>>> niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz >>>> >>>> I read some threads available on your website, but couldn't figured out >>>> a >>>> solution yet. I tried to organize the bvecs in columns, as opposed to >>>> the >>>> original configuration in rows. By doing that and re-launching the >>>> pre-processing command I obtained a differente error message: >>>> Error: bvecs and bvals don't have the same number of entries >>>> >>>> The original bvals and bvecs files seem to have the same numbers of >>>> entries >>>> to me. But the bvecs file produced by the processing - both the >>>> bvecs.norot >>>> and the bvecs files in the dmri folder - don't have all the information >>>> of >>>> the vectors. >>>> >>>> I am enclosing a zip folder with attachments: >>>> 1) original bvecs and bvals files organized in rows and columns >>>> 2) bvecs and bvals files generated by tracula >>>> 3) error logs >>>> >>>> Let me know if you need any other information. >>>> Thanks in advance for your help. >>>> >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>> >> >> _______________________________________________ >> 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. >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > athttp://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. > > > -- > Barbara Kreilkamp > > PhD Candidate > > Magnetic Resonance and Image Analysis Research Center > > University of Liverpool > b.kreilk...@liverpool.ac.uk > http://www.liverpool.ac.uk > > > _______________________________________________ > 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. > >
sages_dmrirc.tutorial
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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.
