Hi Vanessa,
it looks like the error must have occurred earlier in the process as the
input to mri_cc can't be read. Can you send the whole recon-all.log?
cheers
Bruce
On Thu,
16 Jun 2011, Vanessa Lim wrote:
> Hi,
>
>
>
> does anyone know what to do here please? I can see it in file manager.
>
Hi Alan - I dont see the instructions on how QDEC handles this? Could you
point me out to the wiki page that has this info. Again I dont want to draw
manual ROIs instead i want to assign my own value to the color tables
corresponding to the aparc labels in FS.
On Wed, Jun 15, 2011 at 4:28 PM, Alan
Hi Shashwath
you can load a color table from the file menu in tksurfer. We almost
never do this, so I'm not positive it works. The other thing you could do
is read the annotation into matlab and change the color table that is
stored in it, then write it back out.
cheers
Bruce
On Thu, 16 Jun 20
Hi Scott,
You can do trac-all -prep first, to make sure you generate all the files
needed for path reconstruction (including generating priors and masks from
freesurfer recons), then move all your bedpostx files to the dmri.bedpostX
as Anastasia mentioned and then do trac-all -path (for tract
reco
If you're trying to create a label from a volume then use mri_cor2label.
doug
Sudhin A. Shah wrote:
> Hi,
>
> I am trying to use this for the aparc+aseg-in-highres.mgz file instead
> of the default aparc
>
> mri_annotation2label --subject AY --hemi lh --outdir
> $fsfolder/AY/labels this works
>
Hi Actually, its the opposite. I'm trying to get a volume from the label aka
http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/
On 06/16/11, Douglas N Greve wrote:
>
> If you're trying to create a label from a volume then use mri_cor2
Thank you.
I just found this:
http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/
1) Is it better to extract the masks from the .mgz file (as explained on this
site) as opposed to converting the aparc+aseg-inhighres.mgz file to .nii.gz
Hi all,
I am trying to overlay a map on a specific subcortical structure (the
caudate).
-I obtained the surface of the structure using the command:
mri_tessellate structure.nii.gz 1 lh.structure.surf
-then I projected my map on the surface using:
mri_vol2surf --mov map.nii --regheader structure
Are you running the latest release version? Would it be possible to send
us the surface file and the overlay file that crashes?
Best,
Ruopeng
On 6/16/2011 3:34 PM, iac...@nmr.mgh.harvard.edu wrote:
> Hi all,
> I am trying to overlay a map on a specific subcortical structure (the
> caudate).
>
>
Hello,
When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects
Directory, and then reran them using the FS5 recon-all stream. This updated
their subject folders with the FS5 changes, but not in as many places as I
would have thought. For example, on 6 test subjects, I created
Hi guys,
I'm curious why the conform step of mri_convert (in generating
mri/orig.mgz) automatically interpolates oblique acquisitions. Is this
a historical legacy? Something mandated by other elements of the FS
pipeline? As a consequence of this behavior, if you have an oblique
acquisition tha
What atlas does aparc2009 represent?
Regards,
Manish Dalwani
Sr. PRA
Dept. of Psychiatry
University of Colorado
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The information in t
Hi Jeff
what command did you run to run them over?
cheers
Bruce
On Thu, 16 Jun 2011, Jeff Sadino
wrote:
> Hello,
>
> When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects
> Directory, and then reran them using the FS5 recon-all stream. This updated
> their subject folders
it's the version of Christophe Destrieux's atlas he updated in 2009
cheers
Bruce
On Thu, 16 Jun 2011, Dalwani, Manish wrote:
> What atlas does aparc2009 represent?
>
> Regards,
> Manish Dalwani
> Sr. PRA
> Dept. of Psychiatry
> University of Colorado
>
__
Hi Mike,
the intent was to be independent of the prescription of the slices so
that we could always depend on voxel coordinates having some anatomical
meaning, regardless of what crazy slice orientation was prescribed. Not
sure if Doug has some easier work around for you to prevent the rotation
Hello Bruce,
Thank you for your reply. I used recon-all -make all -s subject.
Thanks,
Jeff
On Thu, Jun 16, 2011 at 3:11 PM, Bruce Fischl wrote:
> Hi Jeff
>
> what command did you run to run them over?
>
> cheers
> Bruce
>
> On Thu, 16 Jun 2011, Jeff Sadino wrote:
>
> Hello,
>>
>> When FS5 cam
We recently ran into an issue with Freesurfer's mri_convert tool where it gives
an error of "unsupported slice timing pattern". We have some NIFTI MPRAGE
files that have a "slice_code" with a value of NIFTI_SLICE_ALT_INC2 (=5).
Issue arises in utils/mriio.c (line 9549 of rev:stable5), two slice
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