Hello,
I don't know how can I upload the DICOM Data in Virtuellbox.I installed the
Virtuellbox in windows PC and would like to upload my Image but until now with
out any sucsess. Should I install any extra programm to upload any files?
Thanks for your Feedback.
Best Regards
Sarah
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Hi experts,
I´m trying to convert original images in native space from the LPBA40-Atlas
(http://www.loni.ucla.edu/Atlases/LPBA40/) from img/hdr to nii/nii.gz.
Conversion always results in a left/right flip. Also, mri_convert complains
that no .mat file is available but there are no mat files pr
Dear developers,
I just installed freesurfer 5.1.0 system-wide on one of our clusters.
All of our
users can now access the software, although there is only one license key
in the installation directory. Maybe you prefer that every user on our
system
uses their own license key for your usage stat
Dear FS team,
I am trying to find what is the connection between white matter tracts
with reduced FA and a number of cortical regions/clusters with
significant reduction in cortical thickness from QDEC.
Is there a way to overlap my cortical regions with reduced thickness more
exactly the clus
Hi John
We prefer but don't require that every user download a license
Thanks for asking
Bruce
On Aug 21, 2012, at 9:52 AM, John Donners wrote:
> Dear developers,
>
> I just installed freesurfer 5.1.0 system-wide on one of our clusters.
> All of our
> users can now access the software, altho
Doug,
Thanks for the update and not much time was wasted so no worries. I edited the
brainmask.mgz file and ran the new recon-all command with autorecon-pial, which
created a new brain.finalsurfs.mgz with the dura edited out and correct surfs.
New stat files were created, but no new aparc+aseg.
Dear All,
Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template?
Thank you.
Antonella
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The information in this
Hello, I have a few questions that I hope can be answered:
Q1:How can '.label' files be turned into the necessary '.gca' file needed for
the recon-all pipeline. Starting for the first step in auto-recon2.What else
other than the '.label' files would be needed to create this '.gca' file?
Q2: How
Hi Sarah,
I believe all you need to do is setup a shared directory between Windows
(host OS) and Linux (guest OS - VirtualBox). Then you can copy your DICOM
data to the shared folder and have access to it from within VirtualBox.
Here are some directions which should help:
http://www.virtualbox.
Hi,
I recently installed the updated mri_segstats
(ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux).
This seems to work fine for recalculating the supratentorial volume. However,
it is causing my new recons to fail (see example error below). Any suggestions?
Th
Run it with -autorecon3
doug
On 08/21/2012 10:44 AM, Sarosh, Cyrus wrote:
> Doug,
>
> Thanks for the update and not much time was wasted so no worries. I edited
> the brainmask.mgz file and ran the new recon-all command with autorecon-pial,
> which created a new brain.finalsurfs.mgz with the dur
Sorry, there was a bug in that version. I've put an updated version on
that ftp site
doug
On 08/21/2012 03:49 PM, Blazey, Tyler wrote:
> Hi,
>
> I recently installed the updated mri_segstats
> (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux).
>
> This seems to
1. These need to be image volumes with every voxel containing an index
into FreeSurferColorLUT.txt
2. Use the volumes from 1.
3. Yes.
4. The aseg is used to automated several steps in cortical surface
reconning that you will need to do manually if you don't have one
(ventricle/thalamus/basal
Hi Marco, I think it might be that your PET volume is left-right
reversed. I reran bbregister after left-right reversing the pet data and
it looks much better.
mri_convert PBR_CLBP001_average8-28_BET_hdrOK.nii
--left-right-reverse-pix lrrev.nii
There's always the chance that the T1 was reverse
You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat
doug
On 08/21/2012 11:06 AM, Antonella Kis wrote:
> Dear All,
>
> Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain
> template?
>
> Thank you.
> Antonella
>
>
>
Hi folks, I wanted to make sure i have everything straight w.r.t. the surface
area measures.
as i see there are 4 ways implemented ( somewhere ) to do cortical surface
area analysis.
1. areal expansion
2. Local Gyrification Index
3. direct vertex based true surface area glm, Winkler AM et. al
Hi Greg, I don't know what "areal expansion" refers to. If you want to
use area (eg, the area tab in qdec), you should make sure to download
the most recent version of mris_preproc (which performs a jacobian type
correction)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_pre
ras = (0, 1,
0) k_ras = (0, 0, 1) writing to S01.native.mri.nii.gz...
Thanks for your help,
Janosch
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> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1,
> 0) k_ras = (0, 0, 1) writing to S01.native.mri.nii.gz...
>
>
> Thanks for your help,
>
> Janosch
>
> -- next part -
Regarding Winkler et al.:
http://brainder.org/2012/06/02/facewise-brain-cortical-surface-area-scripts-now-available/
On Aug 21, 2012 11:00 PM, "Gregory Kirk" wrote:
>
> Hi folks, I wanted to make sure i have everything straight w.r.t. the
> surface area measures.
>
> as i see there are 4 ways im
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