Hi Freesurfer expert,
I am looking for just volumetric quantity of *GM,WM,CSF.*
Can u suggest some commands tat i used or explore so that i get volumetric
data.
Presently value for subject* Bert i m getting:*
Right now i m working on mri_segstats >giving me vol of white matter
by using *wm
Please accept my apologies for cross-posting.
I am delighted to advertise the following postdoctoral research position on
behalf of Prof Ed Bullmore at the University of Cambridge.
The job posting is listed at www.jobs.cam.ac.uk/job/3229 and informal
enquiries should be directed via email to Ms K
Hi Matt
if they are outside of the pial surface at the end of recon-all then you
don't have to worry about them.
cheers
Bruce
On Wed, 26 Feb 2014, Moore, Matthew wrote:
Dear Freesurfer Experts,
I am assessing the quality of the initial skull strip for some subject data
after running aut
Dear All,
We have been attempting to run a cross hemisphere analysis using .curv files,
as per the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
I have outlined the exact steps within our pipeline below. When fitting any glm
to the data (simple osgm shown below), we find that across
Hi Saurabh,
That information is automatically calculated for you by FreeSurfer. You
can find more information about it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
Allison
On Wed, 26 Feb 2014, Saurabh Thakur wrote:
Hi Freesurfer expert,
I am looking for just volumetric q
Hi Sabin,
What command did you run? Sending the recon-all.log file in the scripts
dir might be a little more helpful. It's failing because the ribbon.mgz
does not exist which requires surfaces.
This thread might be relevant:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32876
yep, you'll need a new version of mri_segstats, which you can find by
following the thread that Louis posted
doug
On 02/26/2014 12:32 PM, Louis Nicholas Vinke wrote:
> Hi Sabin,
> What command did you run? Sending the recon-all.log file in the
> scripts dir might be a little more helpful. It's
Dear all,
I have a dataset with 1.5T T1 images which have already been skullstriped.
So to avoid the autorecon1 skullstrip, I ran 'recon-all -i subject.nii.gz
-s subject -all -noskullstrip', but it finished with the same error for
more than a dozen of images (example log attached). It says that the
It could be that there is a problem with one or more of your subjects.
First, look at the mask
tksurfer fsaverage_sym lh inflated -overlay mask -fminmax .5 1
the mask should extend over almost all cortex except the medial wall. To
look at each subject, you can run
tksurfer fsaverage_sym lh in
On 02/25/2014 08:34 PM, charujing123 wrote:
> Hidoug,
> Thanks doug.
> For 1st question,I want to reduce the search space of vertex-wise
> analysis to a cluster.
Extract the cluster that you want from the ocn to create a mask, eg, to
get cluster2
mri_binarize --i ocn.mgh --match 2 --o cluster2.m
Try this
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
Don't use -v in this case because -v is for a volumes and volume
overlays and all your data are surface overlays
On 02/25/2014 08:38 PM, charujing123 wrote:
> Hi doug and others,
>
Can you send me
rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh and
/mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/glm/rh.38sb_score.10.mgh
through our file drop https://gate.nmr.mgh.harvard.edu/filedrop2
On 02/26/2014 01:16 AM, charujing123 wrote:
> Hi doug,
> OK.
Good afternoon;
I am hoping you can help me answer a pretty quick
& easy question….
I am trying to identify the best MRI protocol to use
for Freesurfer
analysis… When I look at the FAQ:
Data Requirements
The processing procedures for the creation of
cortical models require
good quali
Hi Douglas
it really depends what you are using it for. MPRAGE and it's variants
work quite well, but for example if you are planning a longitudinal study
you might want a multi-echo mprage to minimize distortions across
session.
cheers
Bruce
On Wed, 26 Feb 2014, Douglas Wojcik wrote:
Dear FreeSurfer experts,
Is it possible to display two labels in tksurfer or freeview, where one label
is outlined with a certain color and the other label is filled with a different
color?
I want to show two labels, one is within the other one.
If yes, could you please tell me the specific st
I'm not sure about freeview, but you cannot do it in tksurfer. You can
take your two labels and create an annotation with mris_label2annot (you
get to specify the color)
doug
On 02/26/2014 05:12 PM, Yang, Daniel wrote:
> Dear FreeSurfer experts,
>
> Is it possible to display two labels in tksu
Doug,
Thanks for your reply! In the annotation, can one of the label be just outlined
and the other filled?
I would really appreciate if you could provide a step-by-step example for this
one… esp. how to create the colorLUT in this case...
Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoc
No, you'd have to modify the label itself to exclude the center (and
create an outline). I don't have any code to do this. For the other
stuff, look at the help for mris_label2annot --help
doug
On 02/26/2014 05:35 PM, Yang, Daniel wrote:
> Doug,
>
> Thanks for your reply! In the annotation, can o
the other thing you could do is draw a path in tksurfer and have it be
the "outline", then load the inner label and display it as filled
On Wed, 26
Feb 2014, Douglas N Greve wrote:
No, you'd have to modify the label itself to exclude the center (and
create an outline). I don't have any code to
Thanks for both of you for the helps! I also find a 3rd solution: convert one
of the labels to mgh and thus use it as overlay and use the other one as label
in freeview.
Doug: Creating an outlined label sounds pretty cool. I wonder whether either
erosion or dilution would do the trick … some so
that's a good way to do it. You don't even need to save it as an mgz. You
can just do tools->labels->copy label stats to overlay, then delete the
label and you have an overlay from it (assuming the label->stat field is
not zero)
On Thu, 27 Feb 2014, Yang, Daniel wrote:
Thanks for both of you
Hi Krista,
Can you please run:
more ~/.Qdecrc
and copy paste the output for me?
The "rm: No match" issue in the qcache is not a problem, it's independent from
the issue of listing lGI in the qdec menu. Even with the no match output in the
qcache command, all the files should have been created
Thanks, Bruce! That is neat!!
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
On 2/26/14 7:03 PM, "Bruce Fischl"
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
that's a good way to do it. You don't even
By the way, what command can I use to erode a label/mgh..?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
On 2/26/14 7:03 PM, "Bruce Fischl"
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
that's a good
mri_morphology for the .mgz
for the label you can do it in tksurfer in the tools->label menu or use
mri_label2label (at least I put it in the dev version, not sure if it is
released yet)
On Thu, 27 Feb 2014, Yang, Daniel wrote:
By the way, what command can I use to erode a label/mgh..?
--
D
Thanks, Bruce! I also found in tksurfer --> Tools --> Labels --> Erode/Dilate
Selected Label !
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
On 2/26/14 8:02 PM, "Bruce Fischl"
mailto:fis...@nmr.m
Thanks doug,
All the best.
Rujing Zha
2014-02-27
charujing123
发件人：Douglas N Greve
发送时间：2014-02-27 01:49
主题：Re: [Freesurfer] questions about ROI analysis
收件人："freesurfer"
抄送：
On 02/25/2014 08:34 PM, charujing123 wrote:
> Hidoug,
> Thanks doug.
> For 1st question,I want to reduce the sea
Hi doug,
Thanks doug.
I am sorry to describe my question no very clearly.It did work,but I want to
view time course of lh.score.thickness.00.mgh vertex by vertex. So I need to
try -v option to view time course manually as you just told me. However I
cannot view anything but darkness when I try
That command definitely will not work. When you ran the command I sent,
did it at least show you something on the surface?
Ruopeng, is there a way to load a surface-based timecourse in freeview?
doug
On 2/26/14 9:11 PM, charujing123 wrote:
Hi doug,
Thanks doug.
I am sorry to describe my
Hi doug and Ruopeng,
Thanks doug.
The command you sent did show something on the surface, but the button of "show
time course" can not be clicked.
Thanks doug and ruopeng.
All the best.
Rujing Zha
2014-02-27
charujing123
发件人：Douglas Greve
发送时间：2014-02-27 11:13
主题：Re: [Freesurfer] time cour
Hello everyone
We are interested in measuring the dimensions of the ventral diencephalon
as part of a general metabolic study. We were wondering how accurate
people consider freesurfer to be at measuring this region currently?
Although some VDC freesurfer results have been published before (Goldm
Dear Freesurfers,
I am using Freesurfer version 5.1 on Linux-centos4_x86_64.
I am trying to set up as SUBJECTS_DIR a folder which is different from
freesurfer's predetermined subjects folder.
my command line was
setenv SUBJECTS_DIR /path/to/my_folder
I get:
bash: setenv: command not found
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