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
- I used the Imaging model HARDI/Q-Ball since these were acquired
using the HARDI method.
I clicked the 'reconstruction' button.
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:
- 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
- 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
- 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
- spline_filter
"/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/track_tmp.trk" 1 "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi.trk"
- 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? RuopengOn 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 -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| * 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> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| <DACC_Insula_WM tracks.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 alanf@bwh.harvard.edu mailto:ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu mailto:afrancis@mclean.harvard.edu
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