Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

good to hear!

On 2/5/19 12:19 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:

     External Email - Use Caution

Hi Doug,

Sorry for the delay in getting back to you. I wanted feedback from the other members of the studies. We all agree that the patch worked wonderfully.

Thanks! François

On 1/24/19, 7:34 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:

 The dev version has the same problem :(

 On 1/24/19 6:37 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
 >          External Email - Use Caution
 >
 > Hi Doug,
 >
 > The data I sent was generated using the development version, freesurfer-linux-centos7_x86_64-dev-20180807-df586ca.  I downloaded the patch and will rerun the scans using version 6.
 >
 > Thanks,
 > François
 >
 >
 > On 1/24/19, 3:40 PM, "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> wrote:
 >
 >      Version 6 does not work very well with such high-res data. I created a
 >      patch for the HCP that you can download from here
 >      ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp
 >      This works in version 6. Just follow the instructions in the README.
 >
 >      I ran it on your data, and it looks pretty good.
 >
 >
 >      On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
 >      >
 >      >         External Email - Use Caution
 >      >
 >      > Hi,
 >      >
 >      > We collected an MP-RAGE scan at .6mm isotropic resolution with the TR
 >      > bumped up to TR=5.  Subject motion artifacts were mitigated by using a
 >      > KinetiCor motion correction system.  We followed the recommendations
 >      > for processing submillimeter scans  described in the FreeSurfer Wiki
 >      > i.e. we added the -cm flag to recon-all and included the mris_inflate
 >      > -n 100 expert option.  The attached PDF of the white matter surfaces
 >      > shows that they appear to be underestimated.  The surface estimates
 >      > fall short of the actual grey/white matter boundary.  Arrows point to
 >      > the most affected areas and the second image is the same as the first
 >      > but without the yellow white matter surface line.  FTP is disabled on
 >      > my government computer.   Please specify the recipient email if I have
 >      > to transfer the file using FileDrop.  Could you suggest other options
 >      > either at the time of scanning or in running recon-all that could help
 >      > better segment the white matter?
 >      >
 >      > Thanks,
 >      >
 >      > François Lalonde, Ph.D.
 >      >
 >      > DNU/HGB/NIMH/NIH
 >      >
 >      > 10 Center Drive, Room 4D18
 >      >
 >      > Bethesda, MD. 20892
 >      >
 >      > flalonde@nih.gov
 >      >
 >      >
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 >
 >
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