Hi Ruopeng: These brains have been run on Tracula and they look good. As a post processing step, I wanted to look at the connectivity between the DACC and anterior insula using DTK and Trackvis. Here is what I did:
1. I used the Imaging model HARDI/Q-Ball since these were acquired using the HARDI method. 2. I clicked the 'reconstruction' button. 3. Next I loaded the dwi.nii.gz I clicked on the load TrackVIS option. I did not fill in any other option. It ran without problems. Here is the script: ************ 11/12/15 1:14 PM ************ Steps to do: 1. hardi_mat "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/matrices/gradient.txt" "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/matrices/temp_mat.dat" -ref "/Users/afrancis/Desktop/Connectome/101309/dmri/dwi.nii.gz" -oc 2. odf_recon "/Users/afrancis/Desktop/Connectome/101309/dmri/dwi.nii.gz" 7 181 "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi" -b0 1 -mat "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/matrices/temp_mat.dat" -p 3 -sn 1 -ot nii 3. odf_tracker "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi" "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/track_tmp.trk" -at 35 -m "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi_dwi.nii" -it nii 4. spline_filter "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/track_tmp.trk" 1 "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi.trk" 5. trackvis "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi.trk" --------- Launching hardi_mat ----------------- Number of measurement points: 6 Number of reconstruction points: 181 --------- Launching odf_recon ----------------- Volume dimension: 145 174 145 Voxel size: 1.250 1.250 1.250 Reading recon matrix... done Matrix file being used: /var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/matrices/temp_mat.dat Reconstructing data... 100% Writing b0 map...Done. Writing dwi map...Done. Reconstruction completed successfully. Time taken: 00:04:43 --------- Launching odf_tracker ----------------- Volume dimension: 145 174 145 Voxel size: 1.250 1.250 1.250 Threshold for mask one: 92.9688 2945 Reading odf max data... 100% Tracking... 100% Time taken: 00:05:40 --------- Launching spline_filter ----------------- Volume dimension: 145 174 145 Voxel size: 1.25 1.25 1.25 Spline filtering track data...Done. Number of tracks: 4586640 --------- Launching trackvis ----------------- TrackVis successfully launched. Total time taken: 00:15:32 However, when I looked at the generated tracks, they looked weirdly straight. I have a hunch that I am processing 'already processed' brains and hence this anomaly. Please advice. Thanks, Alan On Thu, Nov 12, 2015 at 4:20 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > Hi Alan, > > The tracks look weird. Why are they so straight? > > Ruopeng > > On Nov 12, 2015, at 2:14 PM, Alan Francis <alandarkene...@gmail.com> > wrote: > > Hi Anastasia: > > It was great to meet you at the connectivity course at Martinos. I have > been using Trackvis to examine the white matter tracks between the anterior > insula and the Dorsal ACC. In line with your instruction, I created ROIS at > each of these regions. However, the WM tracks generated do not appear to > connect. I have attached a screenshot. > > What is the command that one would use to connect the ROIs? > > thanks so much, > > best regards, > > Alan > > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > *Alan N. Francis PhD* > NIDA T32 Fellow in Computational Neuroscience > Brain Imaging Center > McLean Hospital > Harvard Medical School > 115 Mill Street, Belmont, MA 02478 > al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> > afran...@mclean.harvard.edu > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > <DACC_Insula_WM tracks.png>_______________________________________________ > 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. > > -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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