Hi Bruce,
I have anatomical MRI (MRI 3D T1) and I did recon-all on it.
But when I want to register my CT (image1_CT.nii) with my MRI (using
bbregister), I have an error. When I use my SPECT I have an error too...
Do you have an example of line of command in order to see my faults?
thanks
Dear Freesurfer users,
Recently I started using freesurfer.
My T1-scans are acquired at 1.5T with a resolution of 1x1x1.4 mm (sagittal).
Now I have run into some problems with hippocampal segmentations.
Freesurfer occasionally includes large parts of mostly inferior regions to
the hippocampus
I have added a subject to the to the groups of subject that was
available for the qdec tutorials. with this in mind I have used
make_average_subject and I have now 41 subject. But when I run this
command there is always a subject for which it can not find brain. I am
positive that the
Hi Adam,
No, Freesurfer is not able to extract the neonatal cortical ribbon and I
am not aware of other automatic research tools that would be able to do
that.
Lilla
-- Forwarded message --
Date: Wed, 30 Mar 2011 14:38:26 -0500
From: Eggebrecht, Adam
Hi Marie,
you need to give us the information we need to help you. What error? What
command line did you use? There are lots of examples on the wiki tutorials
and in the help of how to run bbregister
cheers
Bruce
On Thu, 31 Mar 2011, Marie ERESUE wrote:
Hi Bruce,
I have anatomical MRI
can you run ls -l to check that that file exists and you have permission
to it? Also, we need the command line you ran and the error you got in
order to help you.
cheers
Bruce
On Thu, 31 Mar 2011, Knut J Bjuland wrote:
I have added a subject to the to the groups of subject that was
available
Dear Doug and Freesurfer experts,
I have a question related to the previous post. I have two groups
(patients and controls), for which I have both functional and T1 data.
I'd like to look at differences in cortical thickness between the groups
inside some clusters of functional activation.
Would
Hi
I used the followinf commando line optin for make_average_subjects
--fsgd gender_age.fsgd --out fsaverage. I have now used chmod -R +w * to
add write permission to the dir below. As a matter of fate I ran
make_average_subject --subjects 004 --out test and got the same error as
before.
and what is the error?
On Thu, 31 Mar 2011, Knut J Bjuland wrote:
Hi
I used the followinf commando line optin for make_average_subjects --fsgd
gender_age.fsgd --out fsaverage. I have now used chmod -R +w * to add write
permission to the dir below. As a matter of fate I ran
I'm not, either, but I think some good brains are working on it (not mine).
Jason Hill and Andy Knutsen developed a semi-automated method:
http://brainvis.wustl.edu/LIGASE/
On 03/31/2011 07:53 AM, Lilla Zollei wrote:
Hi Adam,
No, Freesurfer is not able to extract the neonatal cortical ribbon
Hi all:
Recently, I have a question about some details of the function
make_average_subject, which creates some average surfaces and volumes based
on the specified subjects' files.
And I'm wondering how it make an average one.
In my opinion, every specified subject's volume and surface register
i used the following command to repeat a failure output. i used just one
subject to get a fast output since my pc is just a core i5 box.
make_average_subject --subjects 004 --out test
INFO: extension is mgz
ERROR: cannot find brain for 004
ERROR: make_average_volume
It appears that the tutorials
Hi Emily, it is just performing a two group analysis, where one of
your groups only has a single subject. There is nothing wrong with what
you did, it all comes down to what conclusion you are trying to draw
from it. I think it is ok for a case report.
doug
Emily Rogalski wrote:
Using q dec
Hi Krishna, if you have a proper freesurfer analysis and registration to
the anatomical, it should work fine.
doug
Krishna Srihasam wrote:
Hi,
Is there a way to use” isxconcat-sess” to average monkey fMRI data?
i.e. I have two groups of monkeys (say, test and control groups) and I
want
You can use mri_binarize with the --match option.
doug
Alexander Lebedev wrote:
*Dear FSL users and developers,*
Please, forgive me for such questions - I am asking because I'm really
stuck with it... Would you be so kind to explain me how can I extract
segmented image with values for
Is this functional (FSFAST) data? Then you can use mri_vol2vol,
something like:
mri_vol2vol --mov fsfast.mni305.nii.gz \
--targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat
--o output.nii.gz
I don't know how the run the FSL
Hi Min,
We've learned that -autorecon2-cp might not be doing what was intended.
Try runing -autorecon2 and see if it fixes everything.
Allison
On Thu, 31 Mar 2011, Min Liu wrote:
Dear Freesurfer users,
My first run of recon12 left some white and grey matter at temporal pole
region excluded.
Thanks Martin!
I will look into why we are not getting a sphere.reg file. Everything else
seems pretty straight forward, although it sounds like the processing will
be a lot easier with FS 5.1. Do you know when we could expect that to be
released?
Best,
Jonathan
On Tue, Mar 29, 2011 at 1:39
Hi Lijie, yes, for the volume averages that is the process (uses the
linear 12 DOF registration to the MNI305). For surfaces, the average
surfaces are created based on the non-linear surface transformation (not
from the average volume).
doug
soft.join Huang wrote:
Hi all:
Recently, I have
Hi Courtney, did you transfer the label to each individual subject using
mri_label2label? A better way to replicate your qdec results is to run
mri_segstats on the input data to qdec (y.mgh usually). Specify the
label with --slabel subject hemi yourlabel. Also specify --avgwf
subjectdata.txt.
Hi Irene, it's not the best way to do it, but it's probably good enough.
A surface-based functional analysis would be better.
doug
Irene Altarelli wrote:
Dear Doug and Freesurfer experts,
I have a question related to the previous post. I have two groups
(patients and controls), for which I
Hi Scott, no there is not another space I would recommend. The cortical
surfaces across subjects don't line up at all with a 12DOF transform. If
you look at your activation in the volume along with surface lines, you
may see that your surfaces intersect some of the activation but not
others. I
That is probably the case that 004 does not have all its files. Some of
the files have been removed to make the distribution smaller. There may
only be enough data to run the tutorial.
doug
Knut J Bjuland wrote:
i used the following command to repeat a failure output. i used just one
subject
Hi Lijie, we have a default surface template that we use. When you
create an average subject from a group, a template based on those
subjects is created at the same time. This can be used as a registration
target.
doug
On 3/31/11 9:03 PM, soft.join Huang wrote:
Thanks for your reply,
Ah, I think I got the point.
Thank you for your quick reply. :)
Lijie Huang
On Fri, Apr 1, 2011 at 10:26 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
Hi Lijie, we have a default surface template that we use. When you create
an average subject from a group, a template based on those
Hi Mayuresh,
I assume you are talking about the area in the posterior midline, where the
pial surface seems to go 'squiggly'. You also seem to have a problem with the
right hemisphere (left visually: I hate radiology ;)), where some dura seems
incorrectly labeled as pial surface (although the
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