Freesurfers,
Anyone saw some errors below from FreeView?
-error
message--
freeview.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion
`a[j].inputstride == vptr->stride' failed.
--
Dear FS peeps,
I am trying to downsample a (white matter) surface with mri_surf2surf. I
also want the output in .tri format.
First problem is that mri_surf2surf doesn't let me output in .tri format
mri_surf2surf --hemi lh --srcsubject subj1 --sval-xyz white --trgsubject
subj1 --trgicoorder 4 -
Dear FreeSurfer list,
I ran recon-all -bert -hippo-subfields, which finished without error.
Now I try to open it with freeview using:
cd $SUBJECTS_DIR/bert/mri
freeview nu.mgz \
-p-labels posterior_left_* posterior_Left-Hippocampus.mgz \
-p-labels posterior_right_* posterior_Right-Hippocampu
can you send us your command line? And does this happen right away, or
after you do something in the interface?
cheers
Bruce
On Thu, 8 Dec 2011, Xinian Zuo wrote:
> Freesurfers,
>
> Anyone saw some errors below from FreeView?
> -error
> mess
Hi John
try adding --tval-xyz so that it knows you want to write out a surface.
cheers
Bruce
On
Thu, 8 Dec 2011, John Griffiths wrote:
Dear FS peeps,
I am trying to downsample a (white matter) surface with mri_surf2surf. I
also want the output in .tri format.
First problem is that mri
h, your data is pretty noisy which I think is the root of why you are
seeing this. I'm not sure we have an easy fix for it though
Bruce
On Tue, 6 Dec
2011, Eun Jin Yoon wrote:
> Hi Bruce,
> I'm using Freesurfer version 5.1.0.
>
> On Dec 6, 2011, at 10:56 AM, Bruce Fischl wrote:
>
>> Hi Eunji
Hi,
Does anyone know how to correctly use the -nomc and -noreg flags?
When I run:
preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc
I get the error message:
ERROR: could not determine file for
/Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr
I also tried
prepr
Hi Paula,
which image are you trying to open? If you're trying to open the merged
files in freeview, you should use the -tv flag for opening it. Did you
source the freesurfer environment before opening freeview? Can you give us
the exact commandline you used?
Priti
> hi,
> i am trying to visuali
Hi Paula,
The * at the end of dtifit_FA.nii.gz may have been a problem (since it
gives an unkown extension error? Extension:146 (Uknown extension))
tcsh
source /software/Freesurfer/5.1.0/SetUpFreeSurfer.csh
freeview -v
/mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz
can
Hi Bruce.
That seems to help - this command runs with no errors
mri_surf2surf --hemi lh --srcsubject CBU070282 --sval-xyz white
--trgsubject CBU070282 --trgicoorder 3 --trgsurfval white_trgicoorder3
--tval-xyz
But unfortunately the --trgicoorder flag doesn't seem to be doing anything;
when I r
Hello;
first, regarding the information here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms
This looks to me very much like snippets of code to help people write their
own code to read and transform files, byte by byte, with the help of the
trackvis .trk header/file spec.
Hi Colin - re: the first question, check out dmri_trk2trk.
Anastasia.
> Hello;
>
> first, regarding the information here:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms
>
> This looks to me very much like snippets of code to help people write
> their
> own code to read
I'll leave this for Doug, but it may be that the target subject has to be
fsaverage (which is the only one that is actually an icosahedron)
cheers
Bruce
On Thu, 8
Dec 2011, John Griffiths wrote:
Hi Bruce.
That seems to help - this command runs with no errors
mri_surf2surf --hemi lh -
Hello Experts,
I would like to be able to get measurements of the anterior portion of the
corona radiata using tracula. Is this a possibility? I did not see it as an
"option" in paths to reconstruct.
thank you very much for your help,
catherine___
Free
Dear Lilla,
I was running the mri_cvs_register with the flag --noaseg and no argument for
my target template so as I understood the registration was done on the cvs
template as you can see below:
mri_cvs_register--mov P01 --noaseg
After registration I got 4 files:
combined_tocvs_avg35_elre
Hi Catherine - Sorry, no hidden options there! We currently have the 18
pathways listed in the tutorial and in our paper. To add another pathway,
it'd have to be labeled manually in the subjects that are part of our
atlas.
a.y
On Thu, 8 Dec 2011, Cat Chong wrote:
> Hello Experts,
>
> I woul
Hi,
We are trying to open something using freeview (ie. freeview -v
SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
When we tried to open it directly from the freeview GUI, it will load
to about 7% and segmentation fault would occur again. We're using
Freesurfer 5.1.0 on Fedor
Yes, this fixes it. Thanks Nick!
> you can try downloading and installing this:
>
>
> http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
>
>
> to install, cp this file to /Applications, then type:
>
> sudo tar zxvf freesurfer-Darw
Dear All:
I am trying to resample my DTI data in the CVS space and seems that after I ran
the mri_cvs_register with the flag --noaseg and no argument for my target
template (so the registration was done on the cvs template) I got the following
error:
ERROR: cannot find or read
/media/1Tra/A
Does it happen with just that file or with other files as well? Would it
be possible to send us that volume file?
Ruopeng
On 12/08/2011 02:03 PM, Xin Zheng wrote:
> Hi,
>
> We are trying to open something using freeview (ie. freeview -v
> SubjectID_template/mri/norm.mgz) and would get a segmenta
can you open it in tkmedit? Sounds like something is wrong with the file
On
Thu, 8 Dec 2011, Xin Zheng wrote:
> Hi,
>
> We are trying to open something using freeview (ie. freeview -v
> SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
> When we tried to open it directly from t
Hi Tenny
That's troubling! What does it give you if you run it with a -v switch?
Is the SUBJECTS_DIR correct? It's one directory above 01_bay6/ and
02_bay6/ directories..
-Krish
On Dec 7, 2011, at 3:10 PM, te...@nmr.mgh.harvard.edu wrote:
> Hi All,
>
> I apologize if this is a simple fix, I
I have no problem loading this file in freeview, in both old and new
versions. Have you used freeview before on the same system? Did it work?
Ruopeng
On 12/08/2011 02:33 PM, Xin Zheng wrote:
> Hi Ruopeng,
>
> It seems to be with all files. Attached is one of them.
>
> Thanks!
> Xin
>
> On Thu, D
Hi,
I have not used freeview before in any version. The images open in
tkmedit. What can we do to diagnose this problem?
Xin
On Thu, Dec 8, 2011 at 3:16 PM, Ruopeng Wang wrote:
> I have no problem loading this file in freeview, in both old and new
> versions. Have you used freeview before on th
Hi Surfers,
It is my first experience with Event-related paradigms. In my
experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum
variable delay between trials to be able to analyze data without any
confound.
Regards
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Ima
Would be hard for us to diagnose if we can't replicate the issue. Is
there any core dump file or some kind of log file that may provide any
hint? From what you described, it seems freeview crashes right when it
is about to render the loaded image. that's about as far as I can guess
now. Is that
Hi,
when I load my ?h.white, inflated, pial, etc data in freeview, I keep
getting this message:
"Surface does not contain valid volume geometry information. It may not
align with volumes and other surfaces"
My command is:
freeview -v fsaverage/mri/aparc+aseg.mgz -f fsaverage/surf/lh.inflated
Hi,
I'm new to tracula, but I'm wondering if I'm overlooking or
misunderstanding the flags. It appears that one types in the trac-all
command 3 times to process a subject (or group of subjects)
>trac-all -prep -c ConfigFile
>trac-all -bedp -c ConfigFile
>trac-all -path -c ConfigFile
Is there a wa
Nope, sorry about that. The reason for keeping them separate is that the
middle step is running bedpostx. It's the lengthiest step and we typically
run it on a cluster. When run on a cluster it's parallelized by slice, and
the other 2 steps are parallelized by subject. One could try to queue up
Hi Antonella,
> I was running the mri_cvs_register with the flag --noaseg and no argument for
> my target template so as I understood the registration was done on the cvs
> template as you can see below:
>
>
> mri_cvs_register--mov P01 --noaseg
Yes, that is right.
> After registration I got
Hi Antonella,
> I am trying to resample my DTI data in the CVS space and seems that after I
> ran the mri_cvs_register with the flag --noaseg and no argument for my target
> template (so the registration was done on the cvs template) I got the
> following error:
>
> ERROR: cannot find or read
H,
I think the warning message says itself very clear :-). If you load a
volume after the surface, it might not align with it because of the lack
of geometry information in the surface header.
I'm not sure about your second question. Anyone?
Ruopeng
On 12/8/11 3:56 PM, kelsi wrote:
Hi,
wh
Thanks, Bruce! The command line is:
freeview --viewsize 500 500 -viewport coronal -slice 1 1 64 -ss
coronal.64.png -v
beijing180/2929166/mri/norm/mgz:opacity=1:grayscale=0,137 -f
beijing180/2929166/surf/lh.white:edgecolor=red -f
beijing180/2929166/surf/rh.white:edgecolor=red
This cmd worked for a
sure, you can probably just email it to me and Ruopeng. Does it work of you
just load it with -f without the other options?
On Fri, 9 Dec 2011,
Xinian Zuo wrote:
> Thanks, Bruce! The command line is:
>
> freeview --viewsize 500 500 -viewport coronal -slice 1 1 64 -ss
> coronal.64.png -v
> beijin
hi all,
this command: mris_convert --combinesurfs lh.pial rh.pial pial.gii.gz
resulted in lh.pial.gii.gz (the help says it should generate pial.gii.gz).
a related question. once i have this gifti file how do i get
annotations+curvature info also into the file? (the gifti schema supports
this rig
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