Hi Shannon, Thank you for the detailed email, outlining some of the aspects of the tutorial that we could improve. We really appreciate your effort in putting these things together and will definitely try to address your concerns to the best of our ability.
Q2. I updated the wiki to correct the typo with the configuration file. It was an oversight on my part. Q4. The Tractography output section (and in general all steps in the tutorial) is targeted keeping in mind, the tracula tutorial data that is available for download. Here we've used one of the training subjects for as an example subject and hence we used only the remaining 32 subjects for training. If you were to use your own data (and not the tutorial data downloaded from the freesurfer website) you would be using all 33 training subjects and hence it should be updated to merged_avg33_mni_flt.mgz (As you're using all 33 subjects for training). I can add a little note in the wiki for people processing their own data about the output file names they should expect. Thanks, Priti > Hi Tracula team, > > > > I have just successfully processed my first scan through > all > the Tracula steps! Though, I have to say it could have gone much smoother > / > quicker if the documentation on the wiki were a little more up-to-date. I > realize it's an ongoing struggle to keep documentation current, so I > thought > I'd send you my observations as I worked through all the bumps in the > road. > You are probably aware of most of these issues but here they are in one > big > email for you to consider: > > > > 1. I'm unable to find anything among the Tracula setup instructions > where it says which version of FSL that Tracula requires, and this version > issue was a crucial piece of the puzzle. I had been failing at step 2 with > an older version of FSL (v4.1.4), and per your suggestion I updated to > v4.1.9. However, when called by Trac-all -bedp, bedpostx ALWAYS failed to > created the "merged*.nii.gz" files for me, even after modifying it and > updating FSL versions. I'm not sure why that is but it may be helpful to > users to know they can simply bypass that step by launching bedpostx > separately in the latest FSL, and pointing it at the "dmri" folder created > during the Trac-all -prep stage. Also, we had to modify "bedpostx", as > well > as "fsl_sub", to get it to launch to our cluster without issues. Once all > the fixes were in place, this step took only an hour or two to run. I then > copied bedpostx's outputs into the requisite "dmri.bedpostX" directory to > launch the -path step, and it completed in about an hour. Launching > "bedpostx_datacheck <dmri folder>" beforehand was very helpful for > troubleshooting the prep stage. > > 2. There is a typo in the description of the configuration file > setup: > "set dorotvecs" is listed in the detailed description under Step9, but > this > is incorrect and will cause errors. It's a bit confusing because it is > correctly listed as "set dorotbvecs" in the complete config file example > you > provide above that section. It's unclear which one is correct and forces > users to debug something which they probably have never run before. > > 3. Also in the config file is the variable $FSLDIR, which I > discovered > we had to set after receiving errors during mni registration. I suppose > the > setting of that variable should be obvious, but it wasn't clear based on > the > example which folder, exactly, should be associated with that variable > name. > We set our $FSLDIR to the /bin folder and all was well. Entirely possible > this is just a lab-specific issue on our end. Since this variable needs > to > be set properly, just like the $SUBJECTS_DIR, perhaps this information > could > be included towards the top of the page where the rest of the required > environmental variables are mentioned? > > 4. Finally, in the "Tractography Outputs" section, the command line > example given needs to be updated because it shows > "lh.ilf_AS_avg32_mni_flt" > as example. The "32" should be "33". The same goes for > "merged_avg32_mni_flt.mgz", obviously. > > > > Until very recently, I was experiencing all the same issues Scott Hayes > has > been reporting lately. (The singular "Data_slice_0002" folder, with > missing > files, and the over-and-over messages of "1 slices processed" in a > terminal > that never throws an error message despite its failure. During the > subsequent -path step, without those "merged*.nii.gz" files, I would > receive > the dreaded & perplexing "Word Too Long" error. A more specific error > message regarding the missing files might be more useful for > troubleshooting > purposes.) > > > > Many thanks for all your advice and help throughout the process! We can > now > move forward and do some exploration... Very exciting! > > > > Shannon T. Buckley > SRA III - Supervisor > CIND, UCSF > 4150 Clement St. (114M) > San Francisco, CA 94121 > Phone: (415) 221-4810 x4251 > Fax: (415) 386-3954 > > > > _______________________________________________ > 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.
