Re: [Freesurfer] vtk to mgz file
Perfect.
now if I wanted to use plotmesh with this, what would the variables be for
x and y: plotmesh('x,y')
On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl
wrote:
>
>
> [aseg,M,mr] = load_mgh('aseg.mgz');
> ind = find(aseg == 16);
>
>
> that will give you the indices in the aseg volume of the voxels that have
> the brainstem label (16). Then you can do what you want with it. The label
> came from $FREESURFER_HOME/FreeSurferColorLUT.txt
>
>
> cheers
> Bruce
>
> On Tue, 19 Jul 2016, Abbie McNulty wrote:
>
> So say I load aseg.mgz into matlab and I want to extract the brainstem in
>> matlab to plot its own volumetric mesh vs. the entire brain, how would I
>> extract
>> the brainstem in matlab?
>>
>> On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> but why not just load the aseg.mgz or whatever volume you are using
>> directly into matlab? Then each structure has a different index that you can
>> extract with the find command
>>
>> cheers
>> Bruce
>> On Tue, 19 Jul 2016, Abbie McNulty wrote:
>>
>> I attached the page in the last message, maybe it didn't
>> show. I guess they aren't called segmentations, but
>> isolation.
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewAnatomicalVolumes
>> This link describes the process that am I am working with,
>> and there is an option to save these isolated pieces, and they save as a
>> .vtk file, I am not
>> converting anything
>>
>> Abbie
>>
>> On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> Hi Abbie
>>
>> I'm not sure what page you mean. The segmentations
>> start life as an .mgz file, so why convert them at all? Just load the
>> aseg.mgz (or whichever
>> segmentation you are interested in) into matlab directly
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 19 Jul 2016, Abbie McNulty wrote:
>>
>> Hi Bruce,
>> So when I'm at this page, I am separating the
>> different parts of the brain so that in the 3D view they show up as their
>> own entity,
>> and I am trying to
>> individually save them. When I press the save
>> button shown on the left hand side of the screen, it saves as a .vtk file,
>> which makes
>> it difficult to upload
>> into matlab. Is there a way to convert this 3D
>> brain piece as an .mgz file?
>>
>> Thanks
>>
>> On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> What segmentation do you mean? Where are you
>> getting vtk files? We write the segmentation into .mgz volumes such as
>> aseg.mgz
>>
>>
>> Cheers
>> Bruce
>>
>>
>> On Jul 18, 2016, at 1:19 PM, Abbie McNulty <
>> amcnu...@stanford.edu> wrote:
>>
>> So we were able to figure out how to
>> segment the different parts of the brain using the bert sample, but have run
>> into another
>> problem.
>> I would like to save each segmentation so that I
>> can import it into matlab and create a matrix in order to create a mesh.
>> The volume
>> segment
>> saves a as a .vtk file, which I don't know how to
>> read into matlab. How can I save it as or convert it to a .mgz file so
>> that I can
>> import it
>> into matlab?
>>
>> Thanks!
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailin
Re: [Freesurfer] vtk to mgz file
If i just wanted to plot the brainstem
On Tue, Jul 19, 2016 at 12:00 PM, Abbie McNulty
wrote:
> Perfect.
> now if I wanted to use plotmesh with this, what would the variables be for
> x and y: plotmesh('x,y')
>
> On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl > wrote:
>
>>
>>
>> [aseg,M,mr] = load_mgh('aseg.mgz');
>> ind = find(aseg == 16);
>>
>>
>> that will give you the indices in the aseg volume of the voxels that have
>> the brainstem label (16). Then you can do what you want with it. The label
>> came from $FREESURFER_HOME/FreeSurferColorLUT.txt
>>
>>
>> cheers
>> Bruce
>>
>> On Tue, 19 Jul 2016, Abbie McNulty wrote:
>>
>> So say I load aseg.mgz into matlab and I want to extract the brainstem in
>>> matlab to plot its own volumetric mesh vs. the entire brain, how would I
>>> extract
>>> the brainstem in matlab?
>>>
>>> On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>> but why not just load the aseg.mgz or whatever volume you are
>>> using directly into matlab? Then each structure has a different index that
>>> you can
>>> extract with the find command
>>>
>>> cheers
>>> Bruce
>>> On Tue, 19 Jul 2016, Abbie McNulty wrote:
>>>
>>> I attached the page in the last message, maybe it didn't
>>> show. I guess they aren't called segmentations, but
>>> isolation.
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewAnatomicalVolumes
>>> This link describes the process that am I am working with,
>>> and there is an option to save these isolated pieces, and they save as a
>>> .vtk file, I am not
>>> converting anything
>>>
>>> Abbie
>>>
>>> On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>> Hi Abbie
>>>
>>> I'm not sure what page you mean. The segmentations
>>> start life as an .mgz file, so why convert them at all? Just load the
>>> aseg.mgz (or whichever
>>> segmentation you are interested in) into matlab
>>> directly
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Tue, 19 Jul 2016, Abbie McNulty wrote:
>>>
>>> Hi Bruce,
>>> So when I'm at this page, I am separating the
>>> different parts of the brain so that in the 3D view they show up as their
>>> own entity,
>>> and I am trying to
>>> individually save them. When I press the save
>>> button shown on the left hand side of the screen, it saves as a .vtk file,
>>> which makes
>>> it difficult to upload
>>> into matlab. Is there a way to convert this 3D
>>> brain piece as an .mgz file?
>>>
>>> Thanks
>>>
>>> On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>> What segmentation do you mean? Where are you
>>> getting vtk files? We write the segmentation into .mgz volumes such as
>>> aseg.mgz
>>>
>>>
>>> Cheers
>>> Bruce
>>>
>>>
>>> On Jul 18, 2016, at 1:19 PM, Abbie McNulty <
>>> amcnu...@stanford.edu> wrote:
>>>
>>> So we were able to figure out how to
>>> segment the different parts of the brain using the bert sample, but have run
>>> into another
>>> problem.
>>> I would like to save each segmentation so that I
>>> can import it into matlab and create a matrix in order to create a mesh.
>>> The volume
>>> segment
>>> saves a as a .vtk file, which I don't know how
>>> to read into matlab. How can I save it as or convert it to a .mgz file so
>>> that I can
>>> impo
Re: [Freesurfer] vtk to mgz file
So say I load aseg.mgz into matlab and I want to extract the brainstem in matlab to plot its own volumetric mesh vs. the entire brain, how would I extract the brainstem in matlab? On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl wrote: > but why not just load the aseg.mgz or whatever volume you are using > directly into matlab? Then each structure has a different index that you > can extract with the find command > > > cheers > Bruce > On Tue, 19 Jul 2016, Abbie McNulty wrote: > > I attached the page in the last message, maybe it didn't show. I guess >> they aren't called segmentations, but >> isolation. >> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewAnatomicalVolumes >> This link describes the process that am I am working with, and there is >> an option to save these isolated pieces, and they save as a .vtk file, I am >> not >> converting anything >> >> Abbie >> >> On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> Hi Abbie >> >> I'm not sure what page you mean. The segmentations start life as an >> .mgz file, so why convert them at all? Just load the aseg.mgz (or whichever >> segmentation you are interested in) into matlab directly >> >> cheers >> Bruce >> >> >> On Tue, 19 Jul 2016, Abbie McNulty wrote: >> >> Hi Bruce, >> So when I'm at this page, I am separating the different parts >> of the brain so that in the 3D view they show up as their own entity, >> and I am trying to >> individually save them. When I press the save button shown on >> the left hand side of the screen, it saves as a .vtk file, which makes >> it difficult to upload >> into matlab. Is there a way to convert this 3D brain piece as >> an .mgz file? >> >> Thanks >> >> On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> What segmentation do you mean? Where are you getting vtk >> files? We write the segmentation into .mgz volumes such as aseg.mgz >> >> >> Cheers >> Bruce >> >> >> On Jul 18, 2016, at 1:19 PM, Abbie McNulty < >> amcnu...@stanford.edu> wrote: >> >> So we were able to figure out how to segment the >> different parts of the brain using the bert sample, but have run into >> another >> problem. >> I would like to save each segmentation so that I can import >> it into matlab and create a matrix in order to create a mesh. The volume >> segment >> saves a as a .vtk file, which I don't know how to read into >> matlab. How can I save it as or convert it to a .mgz file so that I can >> import it >> into matlab? >> >> Thanks! >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> 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. >> >> >> >> >> -- >> Abigail C. McNulty >> Stanford University Class of 2018 >> B.A. Candidate in Bioengineering >> Stanford Women's XC/ Track and Field >> >> >> ___ >> 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 o
Re: [Freesurfer] vtk to mgz file
I attached the page in the last message, maybe it didn't show. I guess they aren't called segmentations, but isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewAnatomicalVolumes This link describes the process that am I am working with, and there is an option to save these isolated pieces, and they save as a .vtk file, I am not converting anything Abbie On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl wrote: > Hi Abbie > > I'm not sure what page you mean. The segmentations start life as an .mgz > file, so why convert them at all? Just load the aseg.mgz (or whichever > segmentation you are interested in) into matlab directly > > cheers > Bruce > > > > On Tue, 19 Jul 2016, Abbie McNulty wrote: > > Hi Bruce, >> So when I'm at this page, I am separating the different parts of the >> brain so that in the 3D view they show up as their own entity, and I am >> trying to >> individually save them. When I press the save button shown on the left >> hand side of the screen, it saves as a .vtk file, which makes it difficult >> to upload >> into matlab. Is there a way to convert this 3D brain piece as an .mgz >> file? >> >> Thanks >> >> On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl >> wrote: >> What segmentation do you mean? Where are you getting vtk files? We write >> the segmentation into .mgz volumes such as aseg.mgz >> >> >> Cheers >> Bruce >> >> >> On Jul 18, 2016, at 1:19 PM, Abbie McNulty wrote: >> >> So we were able to figure out how to segment the different parts of >> the brain using the bert sample, but have run into another problem. >> I would like to save each segmentation so that I can import it into >> matlab and create a matrix in order to create a mesh. The volume segment >> saves a as a .vtk file, which I don't know how to read into matlab. How >> can I save it as or convert it to a .mgz file so that I can import it >> into matlab? >> >> Thanks! >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> 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. >> >> >> >> >> -- >> Abigail C. McNulty >> Stanford University Class of 2018 >> B.A. Candidate in Bioengineering >> Stanford Women's XC/ Track and Field >> >> > ___ > 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. > > -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field ___ 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.
[Freesurfer] vtk to mgz file
So we were able to figure out how to segment the different parts of the brain using the bert sample, but have run into another problem. I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh. The volume segment saves a as a .vtk file, which I don't know how to read into matlab. How can I save it as or convert it to a .mgz file so that I can import it into matlab? Thanks! ___ 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.
Re: [Freesurfer] Freesurfer/Freeview help
Hello, Just a couple more questions that would be great if you could answer in explanation form: How do people develop finite element models from brain MRI? How do people learn and implement the software on an example data set? Abbie On Tue, Jul 5, 2016 at 9:42 AM, Abbie McNulty wrote: > Hello, > > Just a couple more questions that would be great if you could answer in > explanation form: > > How do people develop finite element models from brain MRI? > How do people learn and implement the software on an example data set? > > Abbie > > On Mon, Jun 27, 2016 at 6:37 PM, Bruce Fischl > wrote: > >> Hi Abbie >> >> you just use the recon-all script from the command line: >> >> recon-all \ >> -i \ >> -sd \ >> -s \ >> -all >> >> this will take 5-20 hours and at the end will create and populate a >> directory tree with segmented volumes and surfaces >> cheers >> Bruce >> >> On Mon, 27 Jun >> 2016, Abbie McNulty wrote: >> >> > Hi Bruce, >> > I am trying to create a mesh of the MRI scans, eventually with imported >> > scans, but for now just using the information available through the >> > software. How do you work these voxel segmentations? I'm just very new >> with >> > the software. >> > >> > Say I import an MRI scan, and I want to cortically segment it in order >> to >> > create a mesh of the volume. What are the steps to do this and how do I >> > follow through with each step? I tried to watch the youtube tutorials >> on the >> > Freesurfer youtube, but since they are slides informing of what >> Freesurfer >> > can do and not quite a play-by-play interaction of Freeview, I am stuck. >> > >> > Thanks >> > >> > Abbie >> > >> > On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> > wrote: >> > Hi Abbie >> > >> > what are you trying to create a mesh of? We supply meshes for >> > the >> > gray/white interface and for the pial surface. We supply voxel >> > segmentations of lots of other things that you could mesh, but >> > we don't >> > by default. >> > >> > cheers >> > Bruce >> > On Mon, 27 Jun 2016, Abbie McNulty wrote: >> > >> > > Hello, >> > > I am trying to segment a MRI brain in order to create a mesh >> > of the image >> > > into finite elements, but I am very new with >> > Freesurfer/Freeview and am not >> > > familiar with the tools. So far, I have only uploaded >> > brain.mgt from the >> > > bert file that comes with the program. If I wanted to mesh >> > this brain, how >> > > should I proceed? The online tutorials have confused me >> > especially since I >> > > am not sure if I am supposed to be using the terminal or the >> > command window >> > > for a lot of the code commands. >> > > >> > > Any help would be appreciated. >> > > >> > > Thanks! >> > > >> > > Abbie McNulty >> > > >> > > -- >> > > Abigail C. McNulty >> > > Stanford University Class of 2018 >> > > B.A. Candidate in Bioengineering >> > > Stanford Women's XC/ Track and Field >> > > >> > > >> > ___ >> > 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. >> > >> > >> > >> > >> > -- >> > Abigail C. McNulty >> > Stanford University Class of 2018 >> > B.A
Re: [Freesurfer] Freesurfer/Freeview help
Essentially, once segmentation is achieved, how do you mesh the scans? On Mon, Jun 27, 2016 at 3:41 PM, Abbie McNulty wrote: > Hi Bruce, > > I am trying to create a mesh of the MRI scans, eventually with imported > scans, but for now just using the information available through the > software. How do you work these voxel segmentations? I'm just very new with > the software. > > Say I import an MRI scan, and I want to cortically segment it in order to > create a mesh of the volume. What are the steps to do this and how do I > follow through with each step? I tried to watch the youtube tutorials on > the Freesurfer youtube, but since they are slides informing of what > Freesurfer can do and not quite a play-by-play interaction of Freeview, I > am stuck. > > Thanks > > Abbie > > On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl > wrote: > >> Hi Abbie >> >> what are you trying to create a mesh of? We supply meshes for the >> gray/white interface and for the pial surface. We supply voxel >> segmentations of lots of other things that you could mesh, but we don't >> by default. >> >> cheers >> Bruce >> On Mon, 27 Jun 2016, Abbie McNulty wrote: >> >> > Hello, >> > I am trying to segment a MRI brain in order to create a mesh of the >> image >> > into finite elements, but I am very new with Freesurfer/Freeview and am >> not >> > familiar with the tools. So far, I have only uploaded brain.mgt from the >> > bert file that comes with the program. If I wanted to mesh this brain, >> how >> > should I proceed? The online tutorials have confused me especially >> since I >> > am not sure if I am supposed to be using the terminal or the command >> window >> > for a lot of the code commands. >> > >> > Any help would be appreciated. >> > >> > Thanks! >> > >> > Abbie McNulty >> > >> > -- >> > Abigail C. McNulty >> > Stanford University Class of 2018 >> > B.A. Candidate in Bioengineering >> > Stanford Women's XC/ Track and Field >> > >> > >> ___ >> 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. >> >> > > > -- > Abigail C. McNulty > Stanford University Class of 2018 > B.A. Candidate in Bioengineering > Stanford Women's XC/ Track and Field > -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field ___ 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.
Re: [Freesurfer] Freesurfer/Freeview help
Hi Bruce, I am trying to create a mesh of the MRI scans, eventually with imported scans, but for now just using the information available through the software. How do you work these voxel segmentations? I'm just very new with the software. Say I import an MRI scan, and I want to cortically segment it in order to create a mesh of the volume. What are the steps to do this and how do I follow through with each step? I tried to watch the youtube tutorials on the Freesurfer youtube, but since they are slides informing of what Freesurfer can do and not quite a play-by-play interaction of Freeview, I am stuck. Thanks Abbie On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl wrote: > Hi Abbie > > what are you trying to create a mesh of? We supply meshes for the > gray/white interface and for the pial surface. We supply voxel > segmentations of lots of other things that you could mesh, but we don't > by default. > > cheers > Bruce > On Mon, 27 Jun 2016, Abbie McNulty wrote: > > > Hello, > > I am trying to segment a MRI brain in order to create a mesh of the image > > into finite elements, but I am very new with Freesurfer/Freeview and am > not > > familiar with the tools. So far, I have only uploaded brain.mgt from the > > bert file that comes with the program. If I wanted to mesh this brain, > how > > should I proceed? The online tutorials have confused me especially since > I > > am not sure if I am supposed to be using the terminal or the command > window > > for a lot of the code commands. > > > > Any help would be appreciated. > > > > Thanks! > > > > Abbie McNulty > > > > -- > > Abigail C. McNulty > > Stanford University Class of 2018 > > B.A. Candidate in Bioengineering > > Stanford Women's XC/ Track and Field > > > > > ___ > 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. > > -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field ___ 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.
[Freesurfer] Freesurfer/Freeview help
Hello, I am trying to segment a MRI brain in order to create a mesh of the image into finite elements, but I am very new with Freesurfer/Freeview and am not familiar with the tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh this brain, how should I proceed? The online tutorials have confused me especially since I am not sure if I am supposed to be using the terminal or the command window for a lot of the code commands. Any help would be appreciated. Thanks! Abbie McNulty -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field ___ 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.
