<p dir="ltr">Hi Manuel,</p>
<p dir="ltr">OK, I guess the transform wasn't the issue... The only other possibility I can think of is that the values in the ROI image aren't the expected 0 & 1. Can you load the ROI image in MRView and check that the intensity values outside the ROI are zero and those inside the ROI are one?</p>
<p dir="ltr">Cheers,<br>
Donald</p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: +44 (0)20 7188 7118 ext 53613<br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
<div class="gmail_quote">On 4 Jun 2014 18:06, "Manuel Blesa Cábez" <<a href="mailto:mblesac@gmail.com">mblesac@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Donald,<br><br>This is the mrinfo for the fod:<br><br>************************************************<br>Image: "fod.mif"<br>************************************************<br> Format: MRtrix<br>
Dimensions: 120 x 110 x 54 x 45<br> Voxel size: 1.4 x 1.4 x 2.8 x 1<br> Data type: 32 bit float (little endian)<br> Data strides: [ 2 3 4 1 ]<br> Intensity scaling: offset = 0, multiplier = 1<br>
Comments: FSL5.0<br> Transform: 1 0 0 2.788e+04<br> -0 1 0 -3.487e+04<br> -0 0 1 -5.623e+04<br>
0 0 0 1<br><br><br>The rest of the ROIs, have the same mrinfo that the problematic ROI. I check it with both programs, fslview and mrview and with both looks ok.<br>
<br>To calculate this ROIs I did it with FSL, because i calculated on the template after do the TBSS, to see differences betwen groups, and after this I did the inverse transform to the subject space. Can some of this steps affect to the transform of the ROI?<br>
<br>Regards,<br><br>Manuel Blesa</div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-04 18:54 GMT+02:00 Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Manuel,</p>
<p dir="ltr">The translation column of the transform seems way out - about 30 metres off isocentre... Does the ROI overlay properly onto your fod.mif image within MRView? Does your fod.mif image have the same translation - what does mrinfo report for that image? I expect whatever you used to generate the ROI has corrupted the transform. When you said the ROI looks OK on visual inspection, was that with fslview or MRView? I think fslview just overlays images voxel-wise, with no regard for any differences in the transforms. Basically, if the two images don't overlap in scanner coordinates, then that would explain your issue...</p>
<div>
<p dir="ltr">Cheers,<br>
Donald</p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118" target="_blank">+44 (0)20 7188 7118 ext 53613</a><br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
</div><div><div><div class="gmail_quote">On 4 Jun 2014 17:39, "Manuel Blesa Cábez" <<a href="mailto:mblesac@gmail.com" target="_blank">mblesac@gmail.com</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div><div><div>Hi Donald,<br><br></div>This is the 'mrinfo roi_CC1.mif'<br><br>************************************************<br>Image: "roi_CC1.mif"<br>************************************************<br>
Format: MRtrix<br> Dimensions: 120 x 110 x 54<br> Voxel size: 1.4 x 1.4 x 2.8<br> Data type: 32 bit float (little endian)<br> Data strides: [ -1 2 3 ]<br> Intensity scaling: offset = 0, multiplier = 1<br>
Comments: FSL5.0<br> Transform: 1 0 0 2.788e+04<br> -0 1 0 -3.487e+04<br> -0 0 1 -5.623e+04<br>
0 0 0 1<br><br></div>Regards,<br><br></div>Manuel Blesa<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-04 18:33 GMT+02:00 Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Manuel,</p>
<p dir="ltr">Can you post the output of 'mrinfo roi_CC1.mif' ? Would be good to also have some info as to how the image was generated. Hopefully that'll help to narrow down the problem...</p>
<p dir="ltr">Cheers,<br>
Donald</p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118" target="_blank">+44 (0)20 7188 7118 ext 53613</a><br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
<div class="gmail_quote"><div><div>On 4 Jun 2014 17:01, "Manuel Blesa Cábez" <<a href="mailto:mblesac@gmail.com" target="_blank">mblesac@gmail.com</a>> wrote:<br type="attribution"></div></div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>
<div dir="ltr"><div><div><div><div><div>Hi all,<br><br></div>I have a strange problem, I'm sure is easy to solve but I'm stuck on this and I don't find the solution.<br><br></div>I want to calculate the tracks for a ROI, and when I run it I obtain the following message:<br>
<br>tckgen fod.mif tracks_CC1.tck -algorithm SD_STREAM -grad ag140128a_6_HARDI_WT_ref.b -seed_image roi_CC1.mif -mask mask.mif -number 1000<br><br>tckgen [ERROR]: Cannot use image roi_CC1.mif as ROI - image is empty<br><br>
</div>I opened the ROI and it looks ok, and is not "outside" of the fod map. I did the same, for another ROI and it works correctly. I don't know way this ROI has this problem, Somebody can help me? Maybe is due to the location of the ROI and the default parameters? Thanks in advance.<br>
<br></div>Best regards,<br><br></div>Manuel Blesa<br><div><div><div><br></div></div></div></div>
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