Thanks Anastasia. I figured out the right path, and I'm now running the 2nd step of tracula pipeline on that case. There was a problem with subdirectories (my fault). And also the missing 'SUBJECTS_DIR' syntax in the setenv command, as both you and Barbara pointed out. Thanks again for your help
On Thu, Sep 4, 2014 at 5:22 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Michelle - Try replacing this line: > setenv /Users/michele/Desktop/tracula/sages_diff_test_ > tracula/SD000040_1/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b > > with: > setenv SUBJECTS_DIR /PHShome/my738/FSout > > (Or whatever the location of your freesurfer recons is.) > > > a.y > > On Wed, 3 Sep 2014, Michele Cavallari wrote: > > 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. 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