Ops... I did not see these replies before! Thank you, both!! Christopher, the command line works great. I also found the --viewport and the --ss, which is exactly what I was looking for! I will try the dev version that Anastasia suggested. Thanks a lot, Amelia
-----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Watson, Christopher Sent: Tuesday, March 17, 2015 9:33 PM To: Freesurfer support list; Ruopeng Wang Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts What about: freeview -v FA.nii.gz -v V1.nii.gz:vector=yes ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, March 17, 2015 11:57 AM To: Freesurfer support list; Ruopeng Wang Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts Hi Amelia - Sorry, not that I know of. Perhaps this can be a feature request for Ruopeng to add to freeview :) BTW, freeview in 5.3 had a bug with the vector display for some input image orientations, but this has been fixed in the dev version (that you can download on the web site). a.y On Thu, 12 Mar 2015, Versace, Amelia wrote: > Dear Anastasia, > I was wondering if there is a way to automatically (in command line) derive > the FA/V1 vector image. > fslview FA.nii.gz V1.nii.gz allows to load the FA and V1 image, but then > manual section of the (lines) is needed. > freeview -dti V1 FA does it too (with different xyz convention), > but the 'display as vectors' needs to be manually checked. > Is there any way to produce this image using command line only? Thanks > a lot!! Amelia > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia > Yendiki > Sent: Friday, March 06, 2015 6:56 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts > > > Hi Eileen - It looks like there was a A-P flip introduced to your gradient > vectors. (See screenshot of the tensor eigenvectors. Because they look right > in the coronal view but wrong in the sagittal and axial views, that's why I'm > assuming the flip is in the A-P direction.) To fix this you need to multiply > the y coordinate of your gradient vectors with -1 and rerun. > > If there are still any cases of missing tracts, please look at the bottom of > your dmrirc file for instructions on how to use the reinit parameter (or > search for previous emails on that parameter in the archives). > > Note that your DWI voxel size is anisotropic (finer resolution in x/y than > z), this may cause bias in tractography, so I'd recommend that you switch to > isotropic resolution for future acquisitions if you have control over it. > > Hope this helps, > a.y > > On Fri, 27 Feb 2015, Eileen Moore wrote: > >> Hi Anastasia, >> >> Sorry for the delay -- I missed your response. I did look at the >> anatomical segmentations and thought they looked OK. I've uploaded >> the tracula and corresponding freesurfer data for two subjects: one with >> complete tracts and one with missing/incomplete tracts. I also uploaded my >> dmrirc file. Thanks for taking a look for me. >> >> Eileen. >> >> >> >> Hi Eileen - Have you checked the anatomical segmentations of the >> subjects? The mask that's used by default is the aparc+aseg_mask, >> which comes from registering the cortical parcellationg and subcortical >> segmentation from T1 to diffusion space, and then dilating it by a couple of >> voxels. >> >> If you upload an example data set for me here, I can take a look: >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.har >> vard.edu_filedrop2_&d=BQIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop >> pxeFU&r=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq >> 5C4&m=T2p7z8F4umjzf0YkkzlBSH_xnwrFLJ1rKFdoTAMUxbM&s=TVmCtWOX7TmzlQhiV >> JibKKVtj6CQczyAkyupGnmGZa0&e= Please include all tracula-related >> directories of the subject (dmri, dlabel, etc). >> >> Thanks! >> a.y >> >> On Thu, 18 Dec 2014, Eileen Moore wrote: >> >> Hi - I'm having difficulty with missing or incomplete tracts most of >> my subjects. I'm hoping for suggestions on where I can look for data >> problems. The majority of my subjects have at least one >> missing/incomplete tract, but the specific problematic tract varies >> across subjects (e.g., one subject has a missing L.Uncinate; another >> subject has a missing Forceps Major; another is missing the ILF >> bilaterally, etc.). For my problematic tracts, the path.pd.nii.gz is >> a single line/curve rather than the diffuse volumetric distribution. >> I'm not sure how to correct this. >> >> I have checked my eigenvectors -- the lines appear to be pointing in >> the correct directions in my dtifit_V1 -- so I believe my gradient >> table is correct >> >> I've checked my images for motion via visual inspection and by >> excluding any subjects with dwi_motion outliers in AvgTranslation, >> AvgRotation, PercentBadSlices, and AvgDropoutScore. >> >> I inspected the nodif_brain_mask.nii.gz to look for chunks of >> missing brain and did not identify any problems here. >> >> I've tried increasing the number of control points for each tract. >> >> I'd very much appreciate any suggestions on how to troubleshoot next. >> >> Thank you, >> Eileen. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har >> vard.edu_mailman_listinfo_freesurfer&d=BQIDaQ&c=qS4goWBT7poplM69zy_3x >> hKwEW14JZMSdioCoppxeFU&r=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12 >> A5jbDc-vHb9P3-hkq5C4&m=T2p7z8F4umjzf0YkkzlBSH_xnwrFLJ1rKFdoTAMUxbM&s= >> y_VndM9ft420S4yldRgMbp5txSgs-2Od50SAR78uqHg&e= >> >> >> 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 >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_ >> complianceline&d=BQIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU >> &r=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4&m >> =T2p7z8F4umjzf0YkkzlBSH_xnwrFLJ1rKFdoTAMUxbM&s=2CdcHjq6To7KIChVWGWzdz >> whYh64Rdnt0KgjdlfAops&e= . 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer&d=BQIDaQ&c=qS4goWBT7poplM69zy_3xhK > wEW14JZMSdioCoppxeFU&r=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5j > bDc-vHb9P3-hkq5C4&m=T2p7z8F4umjzf0YkkzlBSH_xnwrFLJ1rKFdoTAMUxbM&s=y_Vn > dM9ft420S4yldRgMbp5txSgs-2Od50SAR78uqHg&e= > > > _______________________________________________ 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
