Hello Anastasia, Everything is fine with the bval and bvec txt files.
I've got an error message in tract statistics when I try to run : trac-all -stat -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial [iMac-de-de:freesurfer/subjects/diffusion_tutorial] GdM% trac-all -stat -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial ERROR: flag -stat unrecognized -stat -c /Applications/freesurfer/subjects/diffusion_tutorial/dmrirc.tutorial The flag -stat is not recognized and I don't know where the stats directory is located ? Please, do you have an idea ? Thanks for your help Best Giovanni 2015-01-07 22:54 GMT+01:00 Giovanni de Marco <demarco.giova...@gmail.com>: > Thanks Anastasia. > I try to rerun trac-all tomorrow. I let you know. > Giovanni > > 2015-01-07 22:50 GMT+01:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu > >: > >> >> This is a plain text file, yes. >> >> On Wed, 7 Jan 2015, Giovanni de Marco wrote: >> >> Please, >>> Could you tell me if this file is better ? I used textwrangler on Imac >>> >>> 2015-01-07 22:36 GMT+01:00 Anastasia Yendiki < >>> ayend...@nmr.mgh.harvard.edu>: >>> >>> Great, then copy these values into a new plain text file (not rich >>> text format), >>> run it through tracula, and let us know what you get. >>> >>> To give you any idea of what I see when I run more on the >>> diffusion60directions.txt that you attached: >>> >>> % more diffusion60directions.txt >>> "diffusion60directions.txt" may be a binary file. See it anyway? >>> book^@^@^@^@mark^@^@^@^@8^@^@^@8^@^@^@D9^F^@^@^@^D^P^@^@^@^@ >>> ^@a^@^@5_ñt¸\ºA^@^@ >>> ^@^@ÿ^?^@^@X8^F^@^D^@^@^@^C^C^@^@^@^D^@^@^L^@^@^@^A^A^@^@ >>> Applications >>> ^@^@^@^A^A^@^@freesurfer^@^@^H^@^@^@^A^A^@^@subjects^G^@^@^ >>> @^A^A^@^@gaitals^@^Y >>> ^@^@^@^A^A^@^@diffusion60directions.txt^@^@^ >>> @^T^@^@^@^A^F^@^@^P^@^@^@$^@^@^@8^@ >>> ^@^@H^@^@^@X^@^@^@^H^@^@^@^D^C^@^@“9$^@^@^@^@^@^H^@^@^@^D^ >>> C^@^@ì^D1^@^@^@^@^@^H >>> ^@^@^@^D^C^@^@©%2^@^@^@^@^@^H^@^@^@^D^C^@^@E^V:^@^@^@^@^@^H^ >>> @^@^@^D^C^@^@;Œ6^@^@^@^@^@^T^@^ >>> @^@^A^F^@^@˜^@^@^@¨^@^@^@¸^@^@^@È^@^@^@Ø^@^@^@^H^@^@^@^@^D^@ >>> ^@A.y^@^@^@^X^@^@^@^A^B^@^@^A^@ >>> ^@^@^@^@^@^@^_^B^@^@^@^@^@^@^_^B^@^@^@^@^@^@^@^@^@^@^A^E^@^@ >>> ^H^@^@^@^A >>> ^@^@file:///^L^@^@^@^A^A^@^@MacintoshH^@^@^@^D^C^@^@^@€œ >>> è^@^@^@^H^@^@^@^@^D^@^@A¹^±Æ^@^@^@$^@^@^@^A^A^@^@E7566EA3-C427-3CD3-93B >>> D-A1F59AF64343^X^@^@^@ >>> >>> >>> On Wed, 7 Jan 2015, Giovanni de Marco wrote: >>> >>> Actually I use this gradient file >>> (diffusion60directions.txt) below >>> with Trackvis and >>> everything is fine. >>> >>> 0 0 0 >>> -0.164494 0.018226 0.98621 >>> -0.190456 0.462978 -0.865666 >>> -0.730086 0.629388 0.266169 >>> -0.613388 -0.746602 0.257566 >>> 0.306915 0.919394 -0.246004 >>> 0.317328 -0.847873 0.424753 >>> 0.965395 0.127917 0.227264 >>> -0.049691 -0.527795 -0.847917 >>> 0.207666 -0.97417 -0.088703 >>> -0.737567 -0.673497 -0.048958 >>> -0.237888 0.330251 0.913424 >>> -0.438285 -0.492274 0.752046 >>> 0 0 0 >>> 0.399147 0.037209 0.916132 >>> -0.463775 0.588699 -0.662078 >>> -0.706111 0.10558 -0.700186 >>> 0.721691 -0.408589 0.558763 >>> 0.614018 0.500213 0.610548 >>> -0.012408 -0.941819 -0.335892 >>> 0.152342 0.987393 0.042982 >>> -0.538071 0.653574 0.532278 >>> 0.033139 0.778743 0.626467 >>> 0.936281 -0.140182 -0.322068 >>> -0.612455 -0.210117 -0.762069 >>> 0.674572 0.218058 -0.705268 >>> 0 0 0 >>> -0.339374 -0.684242 -0.645475 >>> -0.494112 0.845667 0.201743 >>> 0.472146 -0.289458 0.832641 >>> -0.842214 -0.474515 0.255951 >>> 0.077797 -0.973101 0.216848 >>> 0.121406 0.359531 -0.925202 >>> -0.816364 -0.460748 -0.348226 >>> 0.505147 -0.102942 -0.856872 >>> 0.624079 -0.684413 0.376968 >>> 0.158319 -0.724422 0.67093 >>> -0.474079 -0.878731 -0.055503 >>> 0.102353 0.211942 0.971908 >>> 0 0 0 >>> 0.898924 -0.155384 0.409623 >>> -0.405292 -0.747871 0.525763 >>> 0.904768 -0.410581 -0.113222 >>> -0.982422 -0.127045 0.136774 >>> -0.447504 0.884214 -0.133813 >>> -0.862671 0.445789 -0.238897 >>> -0.279017 0.842797 0.460264 >>> -0.546017 0.395479 0.738554 >>> -0.595501 -0.720978 -0.354358 >>> 0.783099 -0.387266 -0.486601 >>> 0.147511 0.645045 -0.749772 >>> 0.403084 0.197286 -0.893645 >>> 0 0 0 >>> -0.985485 0.157362 -0.063694 >>> -0.35289 -0.402766 -0.84454 >>> 0.766668 -0.095163 -0.634952 >>> -0.265955 0.620056 0.738104 >>> 0.078023 0.870617 -0.485736 >>> 0.833015 0.17549 0.524681 >>> -0.720578 0.690754 -0.060215 >>> 0.917014 0.396014 0.047526 >>> -0.140148 0.147395 -0.979098 >>> 0.314193 0.876563 0.364581 >>> 0.874324 0.190397 -0.446439 >>> -0.677724 -0.514302 0.525532 >>> 0 0 0 >>> >>> 2015-01-07 22:21 GMT+01:00 Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> I can see what the name of the file is, but try >>> running "more" >>> on it or opening >>> it with a text editor. >>> >>> On Wed, 7 Jan 2015, Giovanni de Marco wrote: >>> >>> Format txt >>> >>> 2015-01-07 22:08 GMT+01:00 Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> This is not a plain text file. What format >>> is it >>> in? >>> >>> On Wed, 7 Jan 2015, Giovanni de Marco >>> wrote: >>> >>> it looks like thats in attached file >>> >>> 2015-01-07 21:55 GMT+01:00 Anastasia >>> Yendiki >>> <ayend...@nmr.mgh.harvard.edu>: >>> >>> What does the gradient table >>> look >>> like? Based on >>> these errors, >>> it may not like >>> that there is no 0 before the >>> decimal >>> point: >>> >>> printf: -.999989: expected >>> numeric >>> value >>> printf: -.004202: expected >>> numeric >>> value >>> printf: -.001857: expected >>> numeric >>> value >>> >>> >>> On Wed, 7 Jan 2015, Giovanni >>> de Marco >>> wrote: >>> >>> I don't know if you >>> received the >>> zipped log >>> files ? (I >>> received an >>> error message) >>> >>> I send you the most >>> recent log >>> files. >>> >>> See you then >>> >>> Giovanni >>> >>> >>> 2015-01-07 20:57 >>> GMT+01:00 >>> Giovanni de Marco >>> < >>> demarco.giova...@gmail.com>: >>> >>> Please be advised, >>> >>> This message >>> contained one >>> or more of >>> the >>> following >>> prohibited file types: >>> >>> (.zip,.bat,.exe,.pif,.scr). The >>> file(s) have been >>> automatically removed >>> from >>> the message, in >>> order to >>> protect the >>> privacy of >>> our patients >>> and employees, and >>> to protect the >>> integrity >>> of our >>> systems and >>> data. As a >>> security measure to >>> prevent potential >>> viruses >>> and malware, >>> Partners >>> prohibits the >>> receipt of >>> attached files >>> that have >>> the potential >>> to execute >>> malicious >>> code. >>> >>> You should contact >>> the >>> sender, and if >>> you are sure >>> that the >>> original attached >>> file(s) are safe, >>> please >>> use the >>> Partners Secure >>> File Transfer >>> system, >>> >>> https://transfer.partners.org to work >>> with the >>> sender to >>> securely transfer the >>> removed >>> attachment(s). >>> >>> If you do not have >>> an >>> account on the >>> Partners >>> Secure File >>> Transfer System, >>> please register >>> for an >>> account by >>> using the >>> following steps: >>> >>> 1. Go to >>> https://transfer.partners.org >>> 2. Click on "I >>> don't have >>> an account >>> yet" >>> 3. Enter your email >>> address and click >>> “Register” >>> 4. 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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. >>> >>> >>> >>> >>> -- >>> >>> Tel: +33 (0) 6 74 61 01 65 >>> demarco.giova...@gmail.com >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >>> >>> -- >>> >>> Tel: +33 (0) 6 74 61 01 65 >>> demarco.giova...@gmail.com >>> >>> >> _______________________________________________ >> 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. >> >> > > > -- > > Tel: +33 (0) 6 74 61 01 65 > demarco.giova...@gmail.com > -- Tel: +33 (0) 6 74 61 01 65 demarco.giova...@gmail.com
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