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 <rpwang@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 <alandarkenergy@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

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Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu
                                                                                                          
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Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu
                                                                                                          
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