Dear All,
I wonder if you have experienced or there is any report on cortical
segmentation reliability in the mid-line structures of the brain, so one
should take them into consideration in running group differences with Qdec?
Best regards,
Amirhossein Manzouri
Hi Amirhossein
which structures do you mean? Like the ventricles? We usually mask those
regions out using the ?h.cortex.label. The surfaces should be frozen in
those regions in any case, meaning that the white and pial are in the same
location (and the thickness is 0)
cheers
Bruce
On
Hi All,
I ran dt_recon and got the following error. Can someone suggest how to fix this
? I have attached the dwi-infodump.dat file for more information.
Thanks a lot for the help.
Best
Rito
#@#---
Fitting Tensors
Mon Aug 11 07:29:29 EDT 2014
cd
Hi,
Does anyone have recommendations for good automated cortical segmentation
tools for brains with infarct (so some brain missing) or tumors? I am under
the impression that FreeSurfer is not reliable in these cases. If I am
incorrect, any pointers on how to use FreeSurfer in these cases would
hi thank you marie. Ive tried this but it doesnt give me one single spreadsheet
for the value of each subjects lgi, just produces a file in each subjects stats
directory. How do I make a spreadsheet with everybody's lgi values in it?
Kind Wishes,
Melly
From: marie.sch...@unige.ch
To:
Hi Melly,
You can use aparcstats2table from the file you created:
aparcstats2table --subjects …. --hemi lh --meas thickness --parc aparc_lgi
--t summary_lgi.txt
Here you'll read the column thickness in the lh.aparc_lgi.stats file that you
have created with mri_anatomical_stats (i.e.
Question regarding reliability of midline cortical regions by Amir - it refers
to the cingulate cortex, the cuneus, precuneus.
Sincerely
Ivanka Savic M.D., PhD
Professor of Neurology
Karolinska Institute
Dept of Women’s and Children’s Health
and Neurology Clinic,Karolinska Hospital, Q2:07
Just wanted to pose this question again to the Freesurfer community:
Can anyone provide any advice on how to justify using the V1, V2 labels in
FreeSurfer in clinical populations without also collecting functional
retinotopy data?
Thanks!
Krista
-- Forwarded message --
From:
It looks more likely that it is a problem with the skull stripping. If you
clone the brain voxels back in and rerun do things work?
On Aug 11, 2014, at 4:11 PM, Makaretz, Sara Johanna
smakar...@mgh.harvard.edu wrote:
I am having trouble getting a usable brainmask for one of my subjects -
Hi Krista,
Please refer to the following publications from Geoff Aguirre's lab -
http://www.ncbi.nlm.nih.gov/pubmed/23041195
http://www.ncbi.nlm.nih.gov/pubmed/24676149
All templates are in fsaverage_sym space in .mgh format and are available for
download
Katie,
Hi, is the SUBJECTS_DIR set to the proper directory? I see from the
output that it is set to:
SUBJECTS_DIR is
'/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3'
which seems to imply that it might be set to the location of your
freesurfer installation, and not
Hi Nick,
Thanks for responding. We found a solution to the issue with the SUBJECTS_DIR
(which was pointing to the location of our data, not the FS installation).
This issue appeared after doing some software updates on our cluster (including
Ubuntu). Here is how we fixed it:
sudo mv
There's nothing even when the threshold is set to 0.
I just checked the preprocessing outputs. I can see normal-looking volumes
fmcpr.nii.gz
fmcpr.up.nii.gz
fmcpr.up.sm6.mni305.2mm.nii.gz
But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz or
fmcpr.up.sm6.fsaverage.rh.nii.gz
On
did you check the registration?
On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
There's nothing even when the threshold is set to 0.
I just checked the preprocessing outputs. I can see normal-looking
volumes
fmcpr.nii.gz
fmcpr.up.nii.gz
fmcpr.up.sm6.mni305.2mm.nii.gz
But there is nothing
two ways:
1. run tkregister-sess to visually check them
2. look at the first value in register.dof6.dat.mincost. It is hard to
say what a threshold is for a good registration, but typical values are
about .5 or so. If it is .8 or more, it is probably a problem (and
probably the initialization
Both looked fine. First value in .mincost is .45
On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
two ways:
1. run tkregister-sess to visually check them
2. look at the first value in register.dof6.dat.mincost. It is hard to
say what a threshold is for a
How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did not do
this, try it
tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t
fmcpr.up.sm6.fsaverage.lh.nii.gz
This will bring up an overlay as well as a time course
On 08/11/2014 05:05 PM, Jiahe Zhang wrote:
Both
Hi Nick,
We solved this.
Thanks for your help,
Kate
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie
[katie.mclaugh...@childrens.harvard.edu]
Sent: Monday, August 11, 2014 3:42 PM
To:
Hi all,
I have a simple doubt: I am updating my MAC OS X from Snow Leopard to Mavericks.
I am worried if FreeSurfer is going to run perfectly in the new OS X?
Thank you,
Carolina
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Hi, Greg
I use to process my subjects with:
recon-all -s subjid -all -hippo-subfields
The -all flag makes the program run all the 3 stages (autorecon1,
autorecon2 and autorecon3) in sequence. Only after this it starts the
hippo-subfields stage. If you do not have any special reason to run each
Hi, all,
How to calculate the mean cortex thickness of fsaverage?
Thanks!
Wilder___
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