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
<rpw...@nmr.mgh.harvard.edu <mailto: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 <mailto: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
--------- 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
--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
*
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 <mailto:ezra_wegbr...@brown.edu>
afran...@mclean.harvard.edu <mailto:afran...@mclean.harvard.edu>
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<DACC_Insula_WM
tracks.png>_______________________________________________
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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
al...@bwh.harvard.edu <mailto:ezra_wegbr...@brown.edu>
afran...@mclean.harvard.edu <mailto:afran...@mclean.harvard.edu>
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_______________________________________________
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_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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