Hi Julio,
In the past I received this error because the subject was not preprocessed
correctly. Make sure you have a link to the subject's structural recon folder
in the resting state folder. In order to do this, you have to create a txt
file(in this case it would 02_resting/subjectname) and wit
How would I stack them? I found --do-stack only as flag during the registering
and smoothing but not as a command itself.
Thanks,
Clara
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 14. April 2016 18:19:53
Betreff: Re: [Freesurf
Hi Trisanna
you can give the transformation "file" named identity.nofile and it will
assume that the transform is the identity. You can then use mri_vol2label
to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers
Bruce
Hi all
I would like to be certain about what are the algorithms that Freesurfer
use for Segmentation of surfaces (brain-skull-skin), and after, what is the
algorithm for surfaces construction and tessellation?. And moreover i would
like to know if you have some papers about this topic.
Cheers.
Hi Anna
it's tough to tell anything from the surface rendering. You need to go
back through your volumes and see why a chunk of the surface is missing.
The two most likely candidates are the skull stripping (in which case the
brainmask.mgz would be missing this part of the brain) or the topolo
thanks for the replies :)
2016-04-08 15:15 GMT-03:00 Matt Glasser :
> I¹d add that SNR may also change if you don¹t acquire as much data axially
> as you did sagittally. Really it¹s better to acquire your 3D
> T1w/T2w/FLAIR scans sagittally as this is most efficient.
>
> Peace,
>
> Matt.
>
> On
here is a start in case you have insomnia
Dale, A.M., Fischl, B., Sereno, M.I., 1999. Cortical surface-based
analysis. I. Segmentation and surface reconstruction. Neuroimage 9,
179-194.
Dale, A.M., Sereno, M.I., 1993. Improved localization of cortical
activity by combining EEG and MEG wi
Dear all,
I need to compute the geodesic distance (i.,e. the distance on the cortical
surface) between a series of vertices. Specifically, I want to compute the
distance between all the vertices in the right hemisphere (>10) and a
series of vertices of interest (around 2), always located
Hi Joseph
Not sure what youare trying to accomplish but if the beta coefficient for the
timevariable is significant then that means that the slope of change overtime
is significantly different from zero.
Anyway, I think you canestimate subject-specific slopes using lme_mass_rfx
which has as inp
Hi Laura
-Before making anydecision please make sure you correct for multiple
comparisons usinglme_mass_FDR2. That would reduce the likelihood of observing
falsepositives. If very few voxels survived in random unexpected regionsafter
the correction then you can decide to drop that covariate fr
Dear all,
I need to compute the geodesic distance (i.,e. the distance on the cortical
surface) between a series of vertices. Specifically, I want to compute the
distance between all the vertices in the right hemisphere (>10) and a
series of vertices of interest (around 2), always located
Hi Doug,
I have pasted the previous emails below. I have computed mri_segstats to
extract the FA and MD from resampled aparc+aseg.mgz in diffusion space.
-seg-erode 1 was performed during mri_segstats. Now, I will like to
visually inspect the results of that erosion for the left and right
hippocam
Hi Doug,
I edited the registration by hand (after bbregister) in Freeview,
saving the PET_2_T1 volume.
In Freeview (dev FS6) : Tools -> Transform Volume --> Tweaked rotation
and translation --> Save Volume As --> Clicked "Do not resample voxel
data when saving (only update header)"
Using this
joajoajojoa Thanks, chers from Chile
2016-04-15 9:46 GMT-03:00 Bruce Fischl :
> here is a start in case you have insomnia
>
> Dale, A.M., Fischl, B., Sereno, M.I., 1999. Cortical surface-based
> analysis. I. Segmentation and surface reconstruction. Neuroimage 9, 179-194.
>
> Dale, A.M., Seren
Hi Talia. Thanks for the quick answer.
But the preprocessing finished correctly without errors as I can check on
all the log files generated in the same project folder. "subjectname" and
$SUBJECTS_DIR are correctly placed.
The problem is a later step (STEP 5,
http://surfer.nmr.mgh.harvard.edu/fsw
Hi Julio,
You're right in that the problem is occurring in a later step. However, the
fmcpr file is created during preprocessing. When you do the preprocessing step,
it doesn't show an error occurring in the logs(this happened to me too because
it said that preproc-sess was completed but fcseed-
Dear Doug,
One more question:
There are many voxels with negative binding potentials in this dataset,
mostly in the CSF/ventricular regions. Can I restrict the mri_glmfit to
focus only on the voxels with positive BP?
Best Wishes,
Elijah
___
Freesurfer
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you
have contrast in the temporal lobe? Frequently it goes away at 7T due to
dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
things!) expert.
cheers
Bruce
On Fri, 15 Apr 2016, Xiaomin Yue
Thanks for your response. I do have contrast at the temporal lobe. I can
upload the images to your file drop site if you want.
Xiaomin
On Fri, Apr 15, 2016 at 9:08 AM -0700, "Bruce Fischl"
wrote:
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you
h
mri_concat
On 04/15/2016 08:17 AM, Clara Kühn wrote:
> How would I stack them? I found --do-stack only as flag during the
> registering and smoothing but not as a command itself.
> Thanks,
> Clara
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve"
> An: freesurfer@nmr.mgh.harvard.edu
Hi Freesurfer,
Sorry about reposting this email from earlier:
I can't seem to get the TRACULA in the dev version of FS6 to run.
mv -f
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs
mv: rename
/Users/MacPro/Documen
I was hoping the developers might be able to help with a problem I'm having
with a sub-step of preproc-sess.
I executed the following:
preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold
In the relevant output, I see mktemplate-sess completed, followed by a call to
mkbra
thanks Bruce
I could not find identity.nofile anywhere, when I ran mri_vol2surf I got
the following error
trisanna@kaplan:~$ mri_vol2surf --mov
/data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o
/data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh
srcvol = /data-01/trisann
Is your /tmp space full?
On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote:
>
> I was hoping the developers might be able to help with a problem I'm
> having with a sub-step of preproc-sess.
>
>
> I executed the following:
>
> preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd b
what do you want to do exactly? Exclude all voxels if any subject has a
neg BP?
On 04/15/2016 11:55 AM, Elijah Mak wrote:
> Dear Doug,
>
> One more question:
>
> There are many voxels with negative binding potentials in this
> dataset, mostly in the CSF/ventricular regions. Can I restrict the
Hi freesurfers,
I'm having a problem the bvals and bvecs for one of my subject's DTI data.
When I try to run the first step of tracula I get this error message:
"Error: data and bvals/bvecs do not contain the same number of entries"
I have checked, the bvals and bvecs do contain the same amount
No, more like running the voxelwise comparisons only on voxels that have
positive BP between 2 group. Is that possible?
On another note, I am running into a puzzling "Segmentation fault" error
with the following command:
mri_glmfit-sim --glmdir lh_ad_hc.glmdir --cache 2 neg --cwp 0.05
--2spac
I performed the preprocessing again with -per-run parameter. Everything ok
in that step.
The, when I run the fcseed-sess command, I've got new errors.
Segmentation fault
MRIalloc(0, 1, 1): bad parm
I have attached the log file.
2016-04-15 17:56 GMT+02:00 Raney, Talia L. :
> Hi Julio,
> You're
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