Dear freesurfer,
Do you have an existing label of the dorsal part of the premotor cortex? If
not, is it possible to manually label this area?
Best, Silas
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Dear freesurfer,
I was also wondering if you have an existing label of the handknob area located
in primary motor cortex?
Best, Silas
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I want to draw a ROI on a surface and save it as nifti (or which type is needed
to get there).
My original input data is a nifti. For extracting/drawing the visual areas I
project the data on a surface.
> my aim:
In the end I want to have nifti from different visual areas to use them as
masks
Hi Silas
sure, there are tools for drawing ROIs/labels on the surface in tksurfer.
You can create a label on fsaverage or an individual subject, then use
mri_label2label to map it to other subjects if you like
cheers
Bruce
On Thu, 2 Apr 2015,
Silas wrote:
> Dear freesurfer,
>
> Do you have a
no, I don't think we do
sorry
Bruce
On Thu, 2 Apr 2015, Silas wrote:
> Dear freesurfer,
>
> I was also wondering if you have an existing label of the handknob area
> located in primary motor cortex?
>
> Best, Silas
>
>
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Fre
Hi Falko
why not use our estimates of V1/V2 instead? They are far more accurate. I
think tksurfer has a colorwheel option, since we always used it for
retinotopy analysis way back when. But even if not, you should be able to
create the label in tksurfer then import it into freeview, no?
cheers
Hi Doug and Freesurfers,
I ran mri_surfcluster to generate coordinates for cluster maxima from a
functional surface analysis. The summary text file generated by
mri_surfcluster lists a bunch of information about the clusters, including
talairach coordinates for each cluster peak (see example below
Hello Bruce,
I just wanted to touch base regarding the "Indices_oob.nii" subject I had
sent to MGH. Were you by any chance able to detect the issue with running
recon-all on this subject. Thanks in advance for taking a look at this.
Best regards,
Edgar Busovaca
_
Dear all,
I am following the tutorial for group analysis. I successfully ran all the
steps up until the simulation for clusterwise correction. When I attempted
to run the mri_glmfit-sim using the following command in the tutorial:
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \
--cache 4 neg
To advance the field of brain imaging, the HCP was given the unusual NIH
mandate to devote its first two years to rethinking data acquisition and
analysis methods prior to collecting its core dataset. The HCP course
provides an excellent opportunity for brain imagers to profit from this
experience
Dear Freesurfer expert:
I am sorry to disturb you. I am a beginner using freesurfer. I have
calcualted the cortical thickness difference between patients and control group
using the command "mri_glmfit-sim". I found the differences were located in
three cluster: cluster1, cluster2 and clu
Hi Freesurfers,
I'm having some trouble computing the pial layers. Below are the details.
Thanks!
Here is the output from "bugr":
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
RedHat release: CentOS release 6.5 (Final)
K
That data should already be there. If you run mri_glmfit-sim with
--help, look for the description of the csdbase.y.ocn.dat file
On 04/02/2015 01:32 PM, yxin-li wrote:
> Dear Freesurfer expert:
>I am sorry to disturb you. I am a beginner using freesurfer. I
> have calcualted the cortica
Did you run mri_glmfit before that to create lh.gender_age.glmdir ?
On 04/02/2015 12:08 PM, Özlem Ece Demir wrote:
> Dear all,
>
> I am following the tutorial for group analysis. I successfully ran all
> the steps up until the simulation for clusterwise correction. When I
> attempted to run the
You can use mri_label2label and use the --outmask option. If you are
going to use mri_segstats to do the extraction, you can skip the
mri_label2label step and specify the label with --slabel (and add --id 1
otherwise it will give you two ROI results, one in the label, the other
outside the labe
Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
? I might not be able to get to it until after the 13th.
Also, try this as a test:
setenv FS_LOAD_DWI 0
mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh
If that works, you can set that environmen
The limit should be 100. If you run mri_glmfit a 2nd time just with the
missing contrasts, do they appear?
On 04/02/2015 02:34 AM, Bronwyn Overs wrote:
> Dear freesurfer mailing list,
>
> Is there a limit to the number of .mtx files you can feed to
> mri_glmfit? I am running an anlysis with 25 d
You can draw ROIs in tksurfer, save them as a label, then use
mri_label2vol to map the label into a nifti volume. Why do you need a
color wheel for this?
On 04/02/2015 06:57 AM, Kaule, Falko wrote:
> I want to draw a ROI on a surface and save it as nifti (or which type is
> needed to get ther
I think it is just that tksurfer reports coordinates from the orig
surface whereas the cluster summary reports coordinates from the white
surface. We some how never got around to fixing this in tksurfer.
doug
On 04/02/2015 10:18 AM, Alexandra Tanner wrote:
> Hi Doug and Freesurfers,
>
> I ran m
Hello Edgar,
I am going to be looking at your case and seeing if I can replicate the
error. I have your .nii file and will run it through our processing
stream here, but could you send me your subject folder so that I can
look through your files/logs to give me some more information?
You can
Is dcmdjpeg.fs in your path? What are the contents of the file
/tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ?
On 04/02/2015 04:53 PM, A-reum Min wrote:
> Hi doug.
> I try this as a test.
> (here is a my terminal)
> ***
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
then show up these
dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
cannot open shared object file: No such file or directory
dcmjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)
and my sub
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
then show up these
dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
cannot open shared object file: No such file or directory
dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)
and my su
Hi doug
dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
then show up these
dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
cannot open shared object file: No such file or directory
Thank you very much. I have resolved Sess49 (--s) error but the "ERROR: Flag —s
unrecognized" is still remained.
Stefano
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 31-mar-2015 18.07
A:
Ogg: Re: [Freesurfer] isxconcat-sess problem
Not sure what is going wrong with the 1st
do you have another double dash (--s) in the command line?
On 4/3/15 1:00 AM, std...@virgilio.it wrote:
Thank you very much. I have resolved Sess49 (--s) error but the
"ERROR: Flag —s unrecognized" is still remained.
Stefano
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 31-
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