Hi all,
I am using Freesurfer 5.0.0, before the outputs for cortical and
subcortical GM and WM were made available in the final output files.
What is the best way to calculate total gray matter volume (cortical and
subcortical)? Is it through mris_anatomical_stats or mri_segstats? Also,
are there
Dear freesurfer experts,
I am trying to run a volume analysis with qdec. One of my discrete variables
has 3 three levels...Is Freesurfer capable of creating a FSGD file of a
discrete variable like this?
When I m running the analysis, the terminal also says "no contrasts specified"
after trying
Hi Peter
it looks like this is the first error:
GCAMwrite(transforms/talairach.m3z): gzip encountered error.
writing output transformation to transforms/talairach.m3z...
GCAMwrite
GCAMwrite:: m3z loop
GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z
GCAMwrite:: the popen error
Thank you, Sita, for your reply.
1. The skull strip was good, the cortex disappeared after we added cp.
I removed control points and put new ones that are surely in wm, now re-running.
2. I have one more question: I did previous analysis with FS5.0 on
1.5T data with non-isotropic voxels. Now for
Hi Tanja,
yes, 3T will have more dielectric/RF penetration inhomogeneity than 1.5T.
There was also a change to recon-all that caused the control points to be
applied to the subcortical normalize as well as cortical (previously
it was just cortical) that a number of people have now reported mes
Hi Julia, qdec cannot handle 3 levels. You'll have to use the
command-line stream (ie, creating your own fsgd and contrasts and
running mris_preproc, mris_surf2surf, and mri_glmfit).
doug
Richter, Julia wrote:
> Dear freesurfer experts,
>
> I am trying to run a volume analysis with qdec. One of
Hi Peter, that recon-all.log file was empty.
doug
Hellyer, Peter wrote:
> Good Morning, List.
>
> I'm recon-all(ing) a bunch of T1 images using the command recon-all -i
> input.nii.gz -subject name -all -sd /path/to/subject/directory
> Most of the time, these are running just fine, but occasional
Hi
Thanks guys for the reply, I have fixed this now.
ian
> -Original Message-
> From: dgw [mailto:dgwake...@gmail.com]
> Sent: 07 March 2012 19:55
> To: Nick Schmansky
> Cc: Ian Charest; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET:
>
Hi Mark, I don't think thalamic structures were part of the a2005s. I
think it was only cortical structures. The aparc.a2005s+aseg.mgz will
have a whole thalamus segmentation, but that is inherited from the aseg.mgz
doug
Kern, Mark wrote:
> Hi Doug,
>
> Yes, the aparc.a2009s+aseg.mgz files were
Hi all, we're using 5.1 to analyze some single subject, event-related
functional data, and are getting some strangely high values for % signal change
when using func2roi-sess and roisummary-sess.
Here are the commands we're running:
func2roi-sess -s LMV2012_N01_heading -roidef rhmed_singlevsd
Hi Finnegan, there's nothing there that looks wrong with your commands,
but I agree that those values look too high. It is possible that some of
the 12 voxels in the ROI is causing the problem. If you go into the
subject's analysis dir, you'll see a mask there that corresponds to your
ROI. You
Hi Antonella, use cvs_avg35 as the subject and ?h.aparc.annot for the
annotation.
Antonella Kis wrote:
> Hi Doug,
>
> Sorry I bother again I just want to ask you an advice. I was running
> the code which was sent to me by Don:
>
> vals = fs_tal2surf([-16.92 -29.55 34.44]);
> ind_lh = find(vals{1
Thanks Doug.
You mean by subject to define the subject in the fs_tal2surf which by default
is 'subj': FreeSurfer subject
% {default = 'fsaverage'} to be subj = cvs_avg35?
Thanks.
Antonella
From: Douglas N Greve
To: Antonella Kis ; freesurfer
Sent:
Thanks Doug. Looking at the beta.nii.gz values in the mask (assuming the first
N entries in beta correspond to the N events, with nuisance variables after
that), the values for event 18 (which had a particularly high % signal change)
look like:
4.3453
21.4786
16.6500
8.1440
31.
That is just a color lookup table that has an exhaustive list of
possible regions. We do not label all of these, and some of them appear
in some segmentations and not in others. I don't know who (or what
program) does that thalamus labeling (it is not part of a2005s). It is
probably part of th
I think so, although I don't know how Don's program actually works.
doug
Antonella Kis wrote:
>
> Thanks Doug.
>
> You mean by subject to define the subject in the fs_tal2surf which by
> default is 'subj': FreeSurfer subject
> % {default = 'fsaverage'} to be subj = cvs_avg35?
>
> Thanks.
>
Nothing comes to mind. Can you send me the X.mat file in the analysis dir?
Finnegan Calabro wrote:
> Thanks Doug. Looking at the beta.nii.gz values in the mask (assuming the
> first N entries in beta correspond to the N events, with nuisance variables
> after that), the values for event 18 (wh
Hi Freesurfers,
I am trying to use projfrac 1 to threshold my newly created cortical label to
include the entire cortical ribbon since only a small number of voxels are
being included in my manual tracings.
My input code is:
mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nif
Hi Tina, the problem may be with using nifti. Try an mgh file. Also,
you'll probably want to use --projfrac-max 0 1 .1
doug
Tina Jeon wrote:
>
> Hi Freesurfers,
>
>
>
> I am trying to use projfrac 1 to threshold my newly created cortical
> label to include the entire cortical ribbon since only
Hi freesurfers,
I'm getting an error that I don't know how to track down.
Running the following command:
fieldsign-sess -a rtopy.self.lh -sphere -s CP10021_v5
I get the following error:
reading colortable from annotation file...
colortable with 36 entries read (originall
The only thing that I can think of is that the data are really noisy and
you're just getting a really big spread. I computed the efficiency of
condition 18, and it was pretty low. The variance reduction factor was
actually less than 1, meaning that you are actually amplifying the noise
in your
Did you happen to change the surface for your subject between the time
you ran preprocessing and the time you ran fieldsign-sess? It looks like
the number of vertices changed.
doug
Greg Burgess wrote:
> Hi freesurfers,
>
> I'm getting an error that I don't know how to track down.
>
> Running th
It might be ok to do it the way that you suggest. If you have an event
that does not have many presentations, then it will be susceptible to
noise. If you then average that with other events that have many
presentations, then the average will be contaminated and it will be
better to combine the
I ran the surfaces a couple of weeks ago, and I ran all of the fsfast steps
today. I used the -force flag for preproc-sess, mkanalysis-sess, and
selxavg3-sess to make sure that all steps were run rather than leaving old
files in place.
--Greg
On Mar 8, 2012, at 2:06 PM, Douglas N Greve wrote
Greg,
I assume you are using the same surfaces as those that I gave you, right?
Thanks,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greg Burgess
Sent: Thursday, March 08, 2012 2:28 PM
To: Douglas N Gr
can you send the full terminal output?
doug
Greg Burgess wrote:
> I ran the surfaces a couple of weeks ago, and I ran all of the fsfast steps
> today. I used the -force flag for preproc-sess, mkanalysis-sess, and
> selxavg3-sess to make sure that all steps were run rather than leaving old
> fil
Dear All,
I am new to freesurfer DTI analysis. Can anybody explain what is the advantage
of using freesurfer for DTI analysis over DTI studio?
Ayaz
The information contained in this message and any attachments is intended only
for the use of the individual or entity to which it is addressed,
Hi Ayaz
I'm not all that familiar with DTI studio. Tracula, which is a package
within FreeSurfer, automically generates models of 17 or so major white
matter fascicles with no user intervention required.
cheers
Bruce
On Thu, 8 Mar 2012, Ayaz, Muhammad wrote:
Dear All,
I am new to fre
Hi Louis,
Problem solved after installing this package. Thank you!
2012-03-09
Chunhui Chen
_
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875
发件人： Louis Nicholas Vinke
发送时间： 2012-03-06 23:50:05
收件人： chenchunhuic
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