I have two subjects, subA and subB. subA has a binary ROI mask, native
space, that I'd like to place in subB's native space. Both subjects have
been run through all stages of recon, edited, etc. Is there a better or
easier way to achieve this than what I've run?:
#Resample the native space binar
Anyone have any thoughts on this?
On 09/21/2016 04:18 PM, Joel Bruss wrote:
> I have two subjects, subA and subB. subA has a binary ROI mask, native
> space, that I'd like to place in subB's native space. Both subjects have
> been run through all stages of recon, edited, etc
Another bump.
On 09/21/2016 04:18 PM, Joel Bruss wrote:
> I have two subjects, subA and subB. subA has a binary ROI mask, native
> space, that I'd like to place in subB's native space. Both subjects have
> been run through all stages of recon, edited, etc. Is there a better
to redo this using a surface-based label.
>
>
> On 09/29/2016 11:37 AM, Joel Bruss wrote:
>> Another bump.
>>
>> On 09/21/2016 04:18 PM, Joel Bruss wrote:
>>
>>> I have two subjects, subA and subB. subA has a binary ROI mask, native
>>> space, that I&
n freeview. Finally,
> run mri_label2label using the --regmethod surface
>
>
> On 09/29/2016 01:58 PM, Joel Bruss wrote:
>> Ah, I see. The ROI will be subject-dependent (I want to do this for
>> multiple subjects) but the majority, if not all, should be cortical.
>
Doug-
I'm really sorry to keep pestering you about this but I just can't seem
to get this to work. See my replies below:
On 09/30/2016 02:00 PM, Douglas N Greve wrote:
> First, bring up the ROI on the volume along with the surface in the
> volume. You can do this with FreeView. Make sure that t
Sorry, it sent before I finished. I'll try this again.
On 09/30/2016 02:00 PM, Douglas N Greve wrote:
> First, bring up the ROI on the volume along with the surface in the
> volume. You can do this with FreeView. Make sure that the ROI intersects
> the surface.
Yes, this looks fine
> Then run mr
.mgz format made no difference. I see no option for "overlay" in
freeview., I only get that option with tksurfer. The image is blank
when loaded as a volume in freeview. It loads forever when I try to
load it as a surface (I just get the 0-100% progress bar conintually
loading with no end). If
our ROI is binary (0,1), then no voxels would ever appear
> above threshold
>
>
> On 10/03/2016 03:20 PM, Joel Bruss wrote:
>> Sorry, it sent before I finished. I'll try this again.
>>
>> On 09/30/2016 02:00 PM, Douglas N Greve wrote:
>>> First, bring up the
Doug-
Any further thoughts on this?
On 10/05/2016 04:47 PM, Joel Bruss wrote:
> Doug-
>
> I'm sooo close but something isn't right. I've run:
>
> 1)mri_vol2sur to sampel the ROI in subA surface space
>
> 2) mri_cor2label to convert it to a label
>
> 3
Hello-
I'm running freesurfer-Linux-centos4-stable-pub-v4.0.5 on Suse 11.
I've used the output of FreeSurfer, specifically wmparc.mgz to create a
32-bit volume to which I've applied edits. The two commands I used were:
mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o
wmparc-in-native.
I must have posted this to an incorrect address before so I'll try this
again:
Hello-
I'm running freesurfer-Linux-centos4-stable-pub-v4.0.5 on Suse 11.
I've used the output of FreeSurfer, specifically wmparc.mgz to create a
32-bit volume to which I've applied edits. The two commands I used wer
Just a quick question. Is the vitamin E capsule (or whatever the
bright artifact outside
the skull/skin is) denoting the right or left hemisphere for the
Buckner 40-brain data
(look at subject buckner_data/group_study/004/mri/rawavg.mgz)?
Thanks,
Joel
Hello-
I'm running FreeSurfer v4.01on SUSE Linux
I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but
in the native MRI space. I see that the output of "CA Label" produces
a file that is fit to the "CA Normalize" step but I can't figure out
the transform that was used. Specifi
rach space (see mri_convert --help for details).
>
> Nick
>
> On Tue, 2007-11-13 at 12:01 -0600, joel bruss wrote:
>
> > Hello-
> >
> > I'm running FreeSurfer v4.01on SUSE Linux
> >
> > I'm interested in viewing the sub-cortical parcels, /mri/
in
> the subject space, so you should be set.
>
> cheers,
> Bruce
> On Tue, 13 Nov 2007, joel bruss
> wrote:
>
>
> > Hello-
> >
> > I'm running FreeSurfer v4.01on SUSE Linux
> >
> > I'm interested in viewing the sub-cortical parce
I was trying to run a single sujbect through recon-all and got the following
error:
Thu Feb 28 16:34:57 CST 2008
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#
[EMAIL PROTECTED] Talairach Failure Detection Thu Feb 28
Is there a place to download the 40 brains used in the creation of the
Desikan atlas? If so, would the training data have all of the FreeSurfer
data (directories and transform files) so that one could easily create ones
own parcellation scheme and create a new brain?
__
Hello-
Is there anywhere to download the 40 subjects used to create the Desikan
atlas? If so, do these datasets contain all the transform/FreeSurfer files
from start to finish?
Thanks,
Joel
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htt
When FreeSurfer performs the average of 2 or more scans to create rawavg.mgz,
is the 001.mgz used as the target to which all other scans are moved
/averaged to or is there some between-space alignment amongst the scans?
-Joel
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Hello-
I was running recon-all when my machine croaked. I was on the latter-half
of day two and I think (hope) that the process was nearing completion. Is
there a command to give to FreeSurfer to start back in the pipeline where
the process left off or do I have to do each command separately?
Sp
Hello-
I ran recon-all and it reported that everything ran with no errors but, when
I go into mri, there is no wmparc.mgz file. I tried running:
mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon
--o mri/wmparc.mgz --ctxseg aparc+aseg.mgz
and all was running well until it
I'll try this again as I'm stuck and in need of help.
I ran recon-all and it reported that everything ran with no errors but, when
I go into mri, there is no wmparc.mgz file. I tried running:
mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon
--o mri/wmparc.mgz --ctxseg
Not to hijack your question, but I have similar questions. I have CUDA
toolkit 3.1 installed, "cudadetect" returns: "Detecting CUDA... 32767 CUDA
enabled device(s) detected." but, when I run recon-all, e.g.:
recon-all -subjid PC -all -use-gpu
I get the following errors at the mri_em_register_c
he -use-gpu flag
> > in any kind of important group analysis yet.
> >
> > please let of us know though of any problems you encounter. we need to
> > learn what kind of gpu cards people have out there in order to gauge how
> > far we can optimize our routines.
> >
>
> which has the 64b libcudart, and not:
>
> /usr/local/cuda/lib
>
> which has the 32b.
>
> n.
>
>
> On Tue, 2010-08-17 at 12:17 -0500, joel bruss wrote:
> > Nick-
> >
> > I Dl'ed the tarball, unpacked, and re-ran. I r
I have a subject run through recon-all that has gross errors in GM/WM
surfaces. I did my best to follow the ControlPoints tutorial on:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints
My first try had >300 control points with no difference in the WM.mgz
file. I stumbled upon t
I ran across the same issue reported in:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17687.html
The initial question was why mri_segstats did not work and complained:
"Error: could not open stats/aseg/stats for writing"
If you try to, literally, copy and paste the same comm
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