Thanks Bruce. Appreciate all your help.
Kind regards,
Sampada
On Friday, April 8, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sampada
I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm slice data. You might get ok asegs.
sorry Bruce
On Fri, 8 Apr 2016, Dr Sampada Sinha wrote:
Hello Bruce,
Thanks for your reply. Brief history of my problem so far is that: as you noticed before, my images have very low resolution and very less contrast. My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5; dimension 512x512x20. I do run mri_convert to conform it to 1x1x1 mm voxel dimension. But I am getting huge topological defect and in 3-4 patients, and, brain areas are missing as well after running recon-all command. I tried to manually edit those missing brain voxels. But, apart from getting topological error, even after the process is complete, lGI stops running because of high Euler number.
I am trying not to discard those sMRI images. Want to glean at least some data out of it. Will greatly appreciate if I can be guided on this.
Thanks and regards,
Sampada
On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Sampada
could you include our previous corresponance in your emails so Ican keep track of what we were talking about? If your slice thickness is really 6.5mm (or slice thickness + gap) then that is probably the source of your problems. You need something much closer to isotropic
cheers Bruce On Wed, 30 Mar 2016, Dr Sampada Sinha wrote: Hello Bruce, Thanks for following it up. Sorry for tardy response. I amat the mercy of power supply and Internet connectivity here. The details of scans are enclosed as a snapshots. Peculiar thing is that we have processed about 23-24 participants' sMRI having similar scanning parameters and their surface reconstruction is okay. One thing I would like to ask, if I may (?) is that: why am I seeing this problem in this particular participant and why not in other ones that have been processed? All participants so far pre-processed with recon-all have similar sMRI image protocol.
Appreciate all your help! Thanks and kind regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
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-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India