Hi!
Well, as far as I know:
- both are MNI standards
Colin27 is the MNI Colin27 single subject standard
fsaverage is MNI305
My problem with fsaverage was that I couldn't use the transformations made
with the registration matrix after spmregister or bbregister, but I
understand that it de
Hi Bruce,
I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a
cluster (which I access via putty).
It's the only scan that has some kind of a scanner artifact and that
shows this particular problem, therefore I thought there might be a
link.
Thanks,
Anne
>>> Bruce Fischl 24/10/
Hi freesurfer,
We are trying to calculate the total cerebral volume which excludes cerebellum,
brainstem, ventricle and CSF from the aseg.txt. Do we use
CortexVol + CorticalWhiteMatterVol + SubCortGrayVol
Or
CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list)
excep
Hi Anne
you should grab a new version of mris_topo_fixer. Nick or Zeke can post
it for you. The problem may be related to your artifact, but the new one
will at least complete and produce surfaces, although they may not be
accurate and you might have to do some editing.
cheers
Bruce
On Wed
OK, thank you. That would be great.
Can I just run the new topo_fixer within my old freesurfer version?
Cheers,
Anne
>>> Bruce Fischl 24/10/2012 15:15 >>>
Hi Anne
you should grab a new version of mris_topo_fixer. Nick or Zeke can post
it for you. The problem may be related to your artifact, b
yes, that should be fine.
On Wed, 24 Oct 2012, Anne Uhlmann wrote:
OK, thank you. That would be great.
Can I just run the new topo_fixer within my old freesurfer version?
Cheers,
Anne
>>> Bruce Fischl 24/10/2012 15:15 >>>
Hi Anne
you should grab a new version of mris_topo_fixer. Nick or Ze
Hi FreeSurfer people,
I'm considering editing through direct repositioning in freeview (under
tools->reposition surface) for some scans.
After that, do I need to rerun everything through the whole recon-all
pipeline? What would be the command line for that?
Thank you very much,
Pietro
--
Pie
Hi Pietro,
I don't think we've setup a pipeline for that yet. You'll need to rerun the
individual commands after mris_make_surfaces (including mris_thickness to
regenerate the thickness maps)
cheers
Bruce
On Wed, 24 Oct 2012, pietro de rossi wrote:
Hi FreeSurfer people,
I'm considering e
ok,
how do I get a list of all the commands after mrsi_make_surface?
2012/10/24 Bruce Fischl
> Hi Pietro,
>
> I don't think we've setup a pipeline for that yet. You'll need to rerun
> the individual commands after mris_make_surfaces (including mris_thickness
> to regenerate the thickness maps)
look in the recon-all -help output
On Wed, 24 Oct 2012, pietro de rossi
wrote:
ok,
how do I get a list of all the commands after mrsi_make_surface?
2012/10/24 Bruce Fischl
Hi Pietro,
I don't think we've setup a pipeline for that yet. You'll need
to rerun the individual com
thanks!
cheers
2012/10/24 Bruce Fischl
> look in the recon-all -help output
>
> On Wed, 24 Oct 2012, pietro de rossi wrote:
>
> ok,
>> how do I get a list of all the commands after mrsi_make_surface?
>>
>> 2012/10/24 Bruce Fischl
>> Hi Pietro,
>>
>> I don't think we've setup a pip
Dear FreeSurfer experts,I'm wondering if is it possible to make vertex to vertex comparisons for thickness on a group of subjects. In other words, I have a bunch of subjects pre-processed with FS but I would like to make comparisons finding the thickness values at same vertex in all of them. Is thi
Hi Bruce,
I'm having the same error:
export SUBJECTS_DIR=$PWD
recon-all -subjid freesurfer -autorecon1
if: Expression Syntax.
Running on: OS X 10.6.8 using both terminal and X11
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
Thanks in advance,
Skyler
--
Skyler G. Shollenbarger
Graduate
Freesurfer,
I am trying to run trac-all –prep and trac-preproc keeps exiting with errors.
It keeps saying the unwrappedphasemaps must contain at least two volumes. My
data only contains one phase image and 2 magnitude images. Do you know what
could be causing this error or how to get around
Hi Shahin, you can do seed-based analysis. In principle you can do this
with task data, you just need to adjust your conclusions accordingly.
There is no easy to way to only do the analysis on the resting epochs of
a blocked design, if that is what you mean.
doug
On 10/24/2012 12:55 AM, SHAHIN
Hi Ryan, it will depend on the order of the classes in your FSGD file
and the order of the +1s and -1s in your contrast. Can you send your
FSGD file? If you want to do a post-hoc analysis to see where your
interaction is coming from, you can look at csdbase.y.ocn.dat (output
from the simulation
If you can get the AAL labels onto the surface, then the surface-based
registration in mri_label2label would be best.
doug
On 10/24/2012 07:01 AM, Garikoitz Lerma-Usabiaga wrote:
> Hi!
> Well, as far as I know:
> - both are MNI standards
> Colin27 is the MNI Colin27 single subject standard
>
On 10/24/2012 09:01 AM, Zheng Hui wrote:
>
> Hi freesurfer,
>
> We are trying to calculate the total cerebral volume which excludes
> cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use
>
> CortexVol + CorticalWhiteMatterVol + SubCortGrayVol
> Or
> CortexVol + CorticalWhiteMatt
Hi Gabriel, this sounds like a standard surface-based thickness study.
Or am I missing something? In case it is, you can look at the group
analysis tutorial. Basically, you run mris_preproc (which puts all of
your subjects into the fsaverage space and saves a stack of thickness
maps in a single
Can you run it with -debug as the first flag (followed by the rest of
your arguments) and send us the terminal output?
On 10/24/2012 12:04 PM, Skyler Gabriel Shollenbarger wrote:
> Hi Bruce,
>
> I'm having the same error:
>
> export SUBJECTS_DIR=$PWD
> recon-all -subjid freesurfer -autorecon1
> i
Thanks doug But I am not sure if it was the answer. To be more specific, my
subjects did two different tasks within one fmri run. I want to see their
functional connectivity during task 1 and task 2 separately.
If it was resting state, I didn't need to separate my data and a simple
fcseed-config l
Sorry, this type of analysis is not possible with FSFAST. You could
possibly create a new functional volume by extracting the relevant
frames for a condition, then run the functional connectivity on that.
doug
On 10/24/2012 01:23 PM, SHAHIN NASR wrote:
> Thanks doug But I am not sure if it wa
the new mris_topo_fixer is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/
On Wed, 2012-10-24 at 09:22 -0400, Bruce Fischl wrote:
> yes, that should be fine.
>
> On Wed, 24 Oct 2012, Anne Uhlmann wrote:
>
> > OK, thank you. That would be great.
> > Can I ju
they will have the same number of vertices. They will all be in one
file, and each vertex is a vertex in fsaverage space, which each subject
vertex being mapped to the closest vertex in surface-based atlas.
doug
On 10/24/2012 04:34 PM, Gabriel Gonzalez Escamilla wrote:
> Thanks Doug,
>
> Does th
Hi Crystal - This is because of the way the B0 dewarping script is called
during the pre-processing. It assumes that you have 2 phase images instead
of the difference of 2 phase images (which is what you have). The next
version actually accommodates both cases but for now you have 2 options:
Hello FreeSurfer users,
I was finally able to compile mri_em_register successfully from source and
trying to test the build with subject 'bert', I ran into this error
~/freesurfer/bin# ./mri_em_register -uns 3 -mask
$SUBJECTS_DIR/bert/mri/brainmask.mgz $SUBJECTS_DIR/bert/mri/nu.mgz
$FREESURFER
Hi Danny
try downloading a new version of bert. This was a bug we had briefly but
fixed a while ago. Maybe you got a version of bert that was generated
with it?
cheers
Bruce
On Wed, 24 Oct 2012, Kim, Daniel wrote:
> Hello FreeSurfer users,
>
> I was finally able to compile mri_em_register succ
Hello,
I'm trying to run a simple recon on a single T1 dataset, and am not
interested in any quantitative measures (this is just for data presentation
and eventual MRI/CT co-registration). To save time, I tried to skip the CA
registration step, but got the following error:
#---
Hi Matt
you can't skip the careg step if you want an automated recon. It's not
optional. Sorry.
Bruce
On Wed, 24 Oct 2012, Matt Leonard wrote:
Hello,
I'm trying to run a simple recon on a single T1 dataset, and am not interested
in any quantitative measures (this is just for
data presentat
Dear FreeSurfers,
I have a question regarding mri_glmfit: Is it possible to get the residual
data after mri_glmfit?
Thank you very much.
Minjie
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