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 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











--
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India