In your log:

"--------- Launching hardi_mat -----------------

Number of measurement points: 6 "

6 directions will not be enough for a hardi/Qball reconstruction. There is something wrong with your selected gradient table. Which did you choose?

On 11/13/2015 10:16 AM, Alan Francis wrote:

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:

--------- Launching hardi_mat -----------------

Number of measurement points: 6

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

--------- Launching hardi_mat -----------------

Number of measurement points: 6

On Thu, Nov 12, 2015 at 4:20 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto: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 <mailto: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

--------- Launching hardi_mat -----------------


Number of measurement points: 6

, 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 <mailto:ezra_wegbreit@brown.edu>
afrancis@mclean.harvard.edu <mailto:afrancis@mclean.harvard.edu>

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<DACC_Insula_WM
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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 mailto:ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu mailto:afrancis@mclean.harvard.edu

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