Hi Bruce, Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and the size is about 3000x2000x140. (We obtained this brain image using different imaging methods)
Our machine has 16GB RAM. Thanks, Younghoon Kim -- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab ---------------------------------------------- younghoon.h....@gmail.com aktivh...@kaist.ac.kr On July 21, 2016 at 10:35:18 AM, Bruce Fischl (fis...@nmr.mgh.harvard.edu) wrote: is Brain_FS.mgz a segmented volume? How much memory do you have on that machine? On Wed, 20 Jul 2016, Younghoon Kim wrote: > Hi Bruce, > > I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to generate a > surface, but received an error message as below: > > changing type of input volume to 8 bits/voxel... > $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ > $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ > Cannot calloc() > > Would this be because my input data is not compatible with the mri_tessellate > command? > > Thanks, > > Younghoon Kim > > -- > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST > OMICS Lab > Wellman Center, Massachusetts General Hospital > Bouma’s Lab > ---------------------------------------------- > younghoon.h....@gmail.com > aktivh...@kaist.ac.kr > > On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu) wrote: > > If you have a segmented volume, you can use mri_tessellate to create the > surface, then introduce the cut(s) and run mris_flatten -1 on the resulting > patch. You can check out our wiki > > http://surfer.nmr.mgh.harvard.edu/fswiki > > which has info on this process, although the flattening isn't terribly well > documented. You need the -1 flag to tell it to only use that one surface > that you are giving it, and not to assume that the entire FS directory > structure exists. > > cheers > Bruce > > > On Wed, 20 Jul 2016, Younghoon Kim wrote: > > > Hi Bruce, > > > > Great! I’m not an expert in FreeSurfer, so can you give me some advice how > to > > generate a surface of our volumetric data and flatten it? > > > > Thanks, > > > > Younghoon Kim > > > > -- > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST > > OMICS Lab > > Wellman Center, Massachusetts General Hospital > > Bouma’s Lab > > ---------------------------------------------- > > younghoon.h....@gmail.com > > aktivh...@kaist.ac.kr > > > > On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu) > wrote: > > > > HI Younghoon > > > > I guess that could work. You will need to introduce at least one cut if not > > more if you surface has substantial Gaussian curvature > > > > cheers > > Bruce > > > > > > On Wed, > > 20 Jul 2016, Younghoon Kim wrote: > > > > > Hi Bruce, > > > > > > We are only interested in the surface image of the volumetric data. > > > > > > For flattening, we do not care about the interior of the volume, so we > > would like > > > to remove the volume data inside. > > > > > > So what we want is to peel off the surface from the segmented brain area > > and > > > flatten that surface. > > > > > > Thanks, > > > > > > Younghoon Kim > > > > > > -- > > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST > > > OMICS Lab > > > Wellman Center, Massachusetts General Hospital > > > Bouma’s Lab > > > ---------------------------------------------- > > > younghoon.h....@gmail.com > > > aktivh...@kaist.ac.kr > > > > > > On July 20, 2016 at 5:00:55 PM, Bruce Fischl ( fis...@nmr.mgh.harvard.edu) > > wrote: > > > > > > Hi Younghoon > > > > > > what structure are you talking about? In general it doesn't make sense to > > > flatten volumetric structures. We flatten the cortex, which is a folded > > > 2D sheet. What would you do with the interior of the volume? > > > > > > cheers > > > Bruce > > > On Wed, 20 Jul > > > 2016, Younghoon Kim wrote: > > > > > > > Hello, > > > > > > > > We have a volumetric data (mgz file) of a segmented brain region. We > want > > > to detect > > > > the surface of this segmented brain volume (i.e. deep brain region) and > > > flatten it > > > > into a 2D image with its original surface texture. > > > > > > > > We’ve noticed that Freesurfer supports an algorithm to flatten > volumetric > > > data. We > > > > wonder if this could be adapted to our data set. Can anyone offer some > > > advice on > > > > how to apply FreeSurfer to this more generic task? > > > > > > > > Thanks, > > > > > > > > Younghoon Kim > > > > > > > > -- > > > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST > > > > OMICS Lab > > > > Wellman Center, Massachusetts General Hospital > > > > Bouma’s Lab > > > > ---------------------------------------------- > > > > younghoon.h....@gmail.com > > > > aktivh...@kaist.ac.kr > > > > > > > >_______________________________________________ > > > 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 . 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