Hello Bruce,
Please find enclosed snapshots of actual volume and wm_aseg.mgz (horizontal and coronal view). Also in case, if I need to send the image over will you please let me know where do I send it? Appreciate all your help.
Thanks and regards,
Sampada
On Thu, Mar 24, 2016 at 6:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Sampada
wow, something went terribly wrong. Can you post an image of the actual volume and maybe of the wm segmentation?
cheers Bruce
On Thu, 24 Mar 2016, Dr Sampada Sinha wrote:
Hello Bruce,
The recon-all -autorecon2 process exited with the error. The lh inflated no fix image is attached with this email. I am also, attaching the mri_info and recon_all.log with this email. I am basically trying to calculate the lGI of the participants. I was having issues with lGI but, its sorted noe. Will appreciate if I can be guided by you about how to fix this. I found the same kind of surface in another participants.
With thanks and regards,
Sampada
On Tue, Mar 22, 2016 at 10:41 PM, Dr Sampada Sinha < drsampadasinha@gmail.com> wrote: Hello Bruce, Thanks again for your prompt response. We have an official holiday here. Will send the info on Thursday.
Thanks and regards, Sampada Predoctoral student KGMU, Lko India
On haveay, March 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I see
if you have defects that large you should look at the inflated.nofix surface to see what they are. What is your voxel resolution? cheers Bruce On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after running autorecon1. I am presently running the autorecon-2 process. Will get back with the surf files when this process is over. Thank you again for your reply and support. Kind regards, Sampada On Tuesday, March 22, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn't > conform to the 1mm cube isotropic. I am trying to work on it and figure out a > solution. However, if I am not, hope its okay to send you the nifti image. > Thanks and regards, > > Sampada > > > > Rnday, March 20, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > what do you mean by "adding" an oblique angle? If you mean acquiring the > data obliquely you should be fine as long as the voxels are close to 1mm > isotropic. > > cheers > Bruce > On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > > > Dear freesurfer experts, > > Does adding an oblique angle during coronal or axial acquisitions of > T1w > > images lead to topographical errors during mri_fix_topology process? > > > > Thanks and regards, > > > > Sampada > > > > > > > > -- > > Sampada Sinha > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sampada Sinha-- Sampada Sinha
-- Sampada Sinha
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