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 I can 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 am at 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