I don't know of any software that does a better job at that task. You do need to run your subject through the Freesurfer pipeline, which does a lot of stuff. It segments into gray matter, white matter, CSF, etc. And yes -- it generates a map of cortical thickness (distance between gm/wm and pial).
Spend some time digesting the Freesurfer wiki. If you want to do what you want to do, Freesurfer can help. But I still agree with Mike: If your controls and proband subjects were scanned on different scanners, you may have a difficult review process ahead of you when it comes time to publish your results. Something to consider sooner rather than later. On Jul 11, 2016, at 10:36 AM, Dev vasu <[email protected]> wrote: > Dear madam, > > Is there any way to measure the distance from Pial surface boundary with > GM/WM boundary in freesurfer ?. > > > Thanks > Vasudev > > On 11 July 2016 at 17:25, Dierker, Donna <[email protected]> wrote: > Hi Vasudev, > > This question confuses me a bit, I confess, but I would use Freesurfer to > generate cortical thickness measurements from T1w volumes: > > https://surfer.nmr.mgh.harvard.edu/fswiki > > Donna > > > On Jul 11, 2016, at 5:20 AM, Dev vasu <[email protected]> > wrote: > > > Dear Sir, > > > > > > can we used myelin style as a mapping method for Volume to surface mapping > > in wb_command to produce cortical thickness files,Unfortunately i only have > > T1w images and we have not acquired T2w images, i would like to use T1w > > images to generate Cortical thickness , could you please let me know if its > > appropriate way generate them using > > wb_command -volume-to-surface-mapping command and Myelin style mapping > > method ?. > > > > > > > > Thanks > > Vasudev > > > > > > > > On 8 July 2016 at 17:03, Harms, Michael <[email protected]> wrote: > > > > Hi, > > For statistical inference, I would recommend that you look into the PALM > > tool. > > > > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM > > > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: [email protected] > > > > From: Dev vasu <[email protected]> > > Date: Friday, July 8, 2016 at 9:56 AM > > To: "Harms, Michael" <[email protected]> > > Cc: "<[email protected]>" <[email protected]> > > Subject: Re: [HCP-Users] create cortical thickness maps for multiple > > subjects in the same template space > > > > Dear Sir, > > > > Is there any way to quantify the changes in cortical thickness between > > healthy controls and non healthy controls ?. > > > > > > Thanks > > Vasudev > > > > On 8 July 2016 at 16:47, Harms, Michael <[email protected]> wrote: > > > > HI, > > Cortical thickness maps on the surface mesh are already created for you. > > You should analyze/view the thickness on the surface; not try to project > > the thickness back onto the volume. > > > > cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: [email protected] > > > > From: <[email protected]> on behalf of Dev vasu > > <[email protected]> > > Date: Friday, July 8, 2016 at 9:35 AM > > To: "<[email protected]>" <[email protected]> > > Subject: [HCP-Users] create cortical thickness maps for multiple subjects > > in the same template space > > > > Dear Sir /madam, > > > > I am able to successfully run Structural preprocessing pipeline on a group > > of 24 subjects, I would like to know how i can create cortical thickness > > maps for all the subjects in MNI152_T1_0.7mm.nii.gz template. > > > > > > > > Thanks > > Vasudev > > > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > > > > > The materials in this message are private and may contain Protected > > Healthcare Information or other information of a sensitive nature. If you > > are not the intended recipient, be advised that any unauthorized use, > > disclosure, copying or the taking of any action in reliance on the contents > > of this information is strictly prohibited. If you have received this email > > in error, please immediately notify the sender via telephone or return mail. > > > > > > > > > > > > The materials in this message are private and may contain Protected > > Healthcare Information or other information of a sensitive nature. If you > > are not the intended recipient, be advised that any unauthorized use, > > disclosure, copying or the taking of any action in reliance on the contents > > of this information is strictly prohibited. If you have received this email > > in error, please immediately notify the sender via telephone or return mail. > > > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
