Hello,
I have to segment out hippocampus only and calculate its volume. Since
FreeSurfer segments out many sub-cortical structures and their respective
volumes, it takes a lot of time ( more than 10 hours ).
Is there any way to extract a particular sub-cortical structure only from
brain (
Hi,
I have a problem running TRACULA in the pre-processing stage.
The error message is the following;
Loading streamline start ROI from
/usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
niiRead(): error opening file
no, sorry. The contextual information from segmenting everything helps a
lot in improving accuracy, so there is no way to only segment a single
structure.
cheers
Bruce
On Thu, 23 Jan 2014, Tanya Verma wrote:
Hello,
I have to segment out hippocampus only and calculate its volume. Since
Hi,
I would like to ask that why does the Freesurfer takes so much time for
processing particularly autorecon2 ?
Knowing that Freesurfer takes a lot of time for processing, why is it still
used widely by researchers ? For segmentation followed by volume
calculation , does one has to really wait
Hi Tanya
we have always preferenced minimizing manual interactions over computer
time. It takes so long because of its level of automation and its
completeness. This is also why it is so widely used I assume - because it
generates a comprehensive, accurate and automated morphometric assay of
Newer versions also have the ability to run some stages on multiple CPU
cores (with the -openmp cores flag) which speeds certain stages (e.g. in
autorecon2) up considerably. I'm also sure Bruce wouldn't turn down more
resources to hire the programmers needed to make it faster either!
Peace,
Hi all,
I have obtained laterality indices using xhemi analyses and would like to
use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions.
I know to get the FDR threshold from tksurfer, but I want to restrict the
clusters to a certain cluster size. Based on a previous thread (
just add --subject fsaverage_sym
btw, that command does not perform FDR
doug
On 01/23/2014 01:41 PM, krista kelly wrote:
Hi all,
I have obtained laterality indices using xhemi analyses and would like
to use FDR instead of the mri_glmfit-sim suggested in the xhemi
instructions. I know to
Hello,
I am emailing to inquire about whether poor grey/white contrast in one part
of a scan (i.e., the posterior and superior part of the scan; ~parietal
cortex) can be addressed. The contrast in other parts of the scan looks
good and freesurfer does a great job of distinguishing white from
Some pictures would probably be helpful to know what the issue is.
Peace,
Matt.
From: Christine Smith cnsm...@ucsd.edu
Date: Thursday, January 23, 2014 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] poor grey/white distinction in superior part of scan
Hello,
I am
Dear FreeSurfers
I am having some troubles to run step 4 of protocol to thickness
reproducibility. The error message is below:
nf04:~ mris_surface_stats -nsmooth 100 -surf_name
/home/nf04/subjects/t_pac01/su
rf/lh.white -out_name
/home/nf04/subjects/groupstudy/lh_std_60.mgh
Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR
threshold from tksurfer and will use that as my -thmin.
One last thing, how would I view the results of mri_surfclluster in
tksurfer? Would I load the ocn.mgh file? If so, I can't seem to find it.
On Thu, Jan 23, 2014 at 2:02
there are lots of output. You can create an annotation (--oannot),
labels (--olab), copy the input and set nonclusters to 0 (--o), map of
corrected voxel-wise significances (--vwsig), or map of cluster-wise
significances (--cwsig). Of course you can get a simple table of the
output too
The dimension mismatch means that the input data does not match the
surface. It looks like the surface is from an individual but the input
data is from a group analysis (which means fsaverage subject)
On 01/23/2014 02:35 PM, Thiago Junqueira wrote:
Dear FreeSurfers
I am having some troubles
Hi,
We'd like to map the cortical GM ribbon on our original single volume native
space anatomical T1.
The dataset has been run through recon-all -all.
The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz' is the
cortical GM mask
in freesurfer space, correct?
I converted the
Hi Thomas
when you say errors in the hippocampus do you mean the aseg or the
surfaces? If the surfaces, don't worry about them as they are not used in
the hippocampal region. You are probably connecting the temporal lobe to
the main body of the white matter creating a giant defect.
cheers
Hi Mihaela
usually that means the subject was partially but not completely rerun.
You can try using recon-all -s subject -make all
and see if it fixes it
cheers
Bruce
On Thu, 23 Jan 2014,
Mihaela Stefan wrote:
Hello FreeSurfers,
I am trying to run a group analysis with Qdec following
-- Forwarded message --
From: Wanda Truong wanda.truong...@gmail.com
Date: 23 January 2014 16:57
Subject: QDEC error
To: freesurfer@nmr.mgh.harvard.edu
Hello,
I am having trouble with my group analysis using QDEC. I have 3 groups, 72
subjects, and 4 covariates. This is the error
there is something wrong with the format. did you make your qdec table
on a windows machine? If so, convert it to linux format or recreate it
on a linux/mac machine
doug
On 01/23/2014 07:02 PM, Wanda Truong wrote:
-- Forwarded message --
From: *Wanda Truong*
From: Christine Smith cnsm...@ucsd.edu
Date: Thursday, January 23, 2014 3:58 PM
To: Matt Glasser m...@ma-tea.com
Subject: Re: [Freesurfer] poor grey/white distinction in superior part of
scan
Please note that the left and right sides of the brain are flipped for
freesurfer vs the dicom
Hi freesurfer crew,
I found some details through this website
http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/index.htm
about
cortical thickness maps with freesurfer. I have done some reading but can't
really make much sense of how I might do this for a single subject
Is there a way of making a volume like aparc+aseg with the defect labels so
that cortical region where the defects are show up red?
Dr Chris Adamson
Research Officer, Developmental Imaging, Murdoch Childrens Research Institute
Murdoch Childrens Research Institute
Royal Children's Hospital
22 matches
Mail list logo
