hemi and tissue type. Look in
> $FREESURFER_HOME/FreeSurferColorLUT.txt
> for how it works for the aparc+aseg.mgz and the wmparc.mgz. You can embed
> the LUT in the file itself with
> mri_convert file.mgz --ctab yournewLUT file.mgz
>
>
>
> On 2/9/2021 5:30 PM, Vinny K wr
z"
> Use the last one ( the one that creates wmparc.mgz) as your template to
> create your new wmBA.mgz file, modifying it as needed.
> You will need to create a new LUT, but let's do that when you get there
>
> On 2/9/2021 10:26 AM, Vinny K wrote:
>
> External
External Email - Use Caution
I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve
wrote:
> which version of FS are you using?
>
> On 2/5/2021 10:02 PM, Vinny K wrote:
>
> External Email - Use
External Email - Use Caution
Hello,
I'd like to obtain white matter parcellations of the Brodmann areas. I am
not certain that the generated wmparc file from recon-all has this type of
parcellation. I was able to convert Brodmann area label files to mgz
format using
sTutorial/TopologicalDefect_freeview
>
>
> On 8/30/20 7:16 AM, Vinny K wrote:
>
> External Email - Use Caution
> Hi,
>
> I've tried to process a scan but it gets hung up on a particular large
> defect and then exits with error. I've had large defects with other scans
> be
External Email - Use Caution
Thank you very much, the modifications worked.
On Thu, Jun 25, 2020 at 10:08 AM Douglas N. Greve
wrote:
> Try using dwi.nii
> Also, you may want to remove -it siemens_dicom
>
>
> On 6/24/2020 6:54 PM, Vinny K wrote:
>
>
External Email - Use Caution
Hi,
I have diffusion-weighted images (DWI) from a Siemens scanner in the .IMA
format. I used the following command in an attempt to convert the DWI
series from .IMA to .nii/.nii.gz format
mri_convert -it siemens_dicom -ot nii
,
Vinny
On Sat, Nov 16, 2019 at 4:56 PM Vinny K
wrote:
> Hi,
>
> I ran the mri_cvs_register between two subjectIDs with very good alignment
> between them. I had assumed that applying the outputted m3z transform,
> i.e.,final _CVSmorph_toTEMPLATE.m3z, to the moving subjectID
External Email - Use Caution
Hi,
I ran the mri_cvs_register between two subjectIDs with very good alignment
between them. I had assumed that applying the outputted m3z transform,
i.e.,final _CVSmorph_toTEMPLATE.m3z, to the moving subjectID (subjb) would
normalize it to the
External Email - Use Caution
Hi,
I figured out the mistake. I had to remove the forward slashes from the
command line. Its running fine now.
Thanks,
Vinny
On Sat, Nov 16, 2019 at 12:13 AM Vinny K
wrote:
> Hi,
>
> The moving subjectid directory (subjb) has a c
Razmara wrote:
> External Email - Use Caution
>
> Hi
> Check your subject and template address directory.
>
>
> On Sat, 16 Nov 2019, 01:05 Vinny K
>> External Email - Use Caution
>>
>> Hi,
>>
>> I'm using the development version
External Email - Use Caution
Hi,
I'm using the development version of FreeSurfer and am attempting to
register two subjects using mri_cvs_register.
This is the command I ran:
mri_cvs_register --mov subjb/ --template subja/
Below was the outputted message:
The outdir:
f running some other nonlinear warping like ANTS or VoxelMorph
> to propagate the labels.
>
> cheers
> Bruce
> On Sat, 19 Oct 2019, Vinny K wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> > I'm looking at diencephalic a
,
Vinny
On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl
wrote:
> Hi Vinny
>
> why do you need to brain structures from MNI space? Isn't the aseg
> sufficient? Or are there structures that are not in the aseg?
>
> cheers
> Bruce
> On Sat, 19 Oct
> 2019, Vinny K wrote:
>
External Email - Use Caution
Hi,
FreeSurfer does a great job in registering atlas structures to patients
with big ventricles. I'd like to use the calculated FreeSurfer transforms
in bringing additional subcortical structures from MNI space (either MNI305
or MNI2009b) into native
eneral mri_binarize --match allows you to
> create an ROI from all the voxels in a segmentation map that have a
> specific segmentation ID.
>
> a.y
>
> On Sep 25, 2018 7:33 AM, Vinny K wrote:
>
> External Email - Use Caution
>
> Hello Anastasia,
>
> The a
these thalamic labels?
Thanks/Vinny
On Thu, Sep 20, 2018 at 8:32 AM Vinny K
wrote:
> Thanks Anastasia, I'll give this approach a try.
>
> On Thu, Sep 20, 2018 at 8:31 AM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> That's correct! You can source the setup scri
-
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Vinny K <
> vinit.k.srivast...@gmail.com>
> *Sent:* Thursday, September 20, 2018 8:25:31 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] error wit
ersion (a feature that you needed and wasn't working in the stable one),
> please use the stable one in general.
>
>
> Best,
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> o
entire log file (scripts/trac-all.log)?
>
> Best,
> a.y
>
> On Sep 19, 2018 8:39 PM, Vinny K wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
>
> I get the following error when ru
entire log file (scripts/trac-all.log)?
>
> Best,
> a.y
>
> On Sep 19, 2018 8:39 PM, Vinny K wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
>
> I get the following error when ru
External Email - Use Caution
Hi,
I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
I get the following error when running the command: trac-all -prep -c
dmrirc.
Any help would be greatly appreciated.
Thanks,
Vinny
External Email - Use Caution
Actually, I was able to match the boundaries with the referenced
publication. So it's all good, thanks again for your help!
Vinny
On Mon, Sep 10, 2018 at 6:55 PM Vinny K
wrote:
> Hi Eugenio,
>
> Thank you for your reply. Somehow the dis
;
> Hi Vinny,
> The anatomical definitions can be found in the paper, which is open access
> (see Table 2):
> https://www.sciencedirect.com/science/article/pii/S1053811918307109
> Kind regards
> Eugenio
>
>
>
> Sent from my phone, please excuse brevity and typos
External Email - Use Caution
Hi,
I ran recon-all to generate the required files for the thalamic
segmentation tool (http://freesurfer.net/fswiki/ThalamicNuclei) using the
latest development version of Freesurfer (06/09/2018) linux-cent06. The
segmented thalamic nuclei were
25 matches
Mail list logo
