Hi all,
I am doing cortical thickness and surface area analyses and had a few
questions regarding editing the borders.
1) Is it reasonable to edit every (big and small) error that I find?
Basically, how much a difference would it make in terms of the surface area
and cortical thickness values if
Just wanted to resend these questions to see if anyone has any answers.
Thanks!
I am doing cortical thickness and surface area analyses and had a few
questions regarding editing the borders.
1) Is it reasonable to edit every (big and small) error that I find?
Basically, how much a difference
at 6:35 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
How did you do the transfer? What was your cmd line?
doug
On 09/10/2013 05:31 PM, krista kelly wrote:
Hello,
I am looking at cortical thickness and surface area using Freesurfer.
I have transferred label V1 from freesurfer onto
this subject and we
will take a look?
thanks
Bruce
On Wed, 2 Oct 2013, krista kelly wrote:
Hi Bruce,
I've tried twice to post this to the freesurfer mail list but it hasn't
worked, I'm assuming because of the attached pictures. I'm going to try
this
again with only one picture and see
Thanks Allison,
So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and
then rerun recon-all from the normalization step? However, I'm not sure how
to run recon starting from the normalization stage. Would you be able to
help with that?
Also, I've been doing manual edits to
Also, just to add to this, if I rerun recon in 5.1 starting from the
normalization stage when I initially ran all subjects in 5.0, will this be
a problem?
On Wed, Oct 9, 2013 at 8:05 PM, krista kelly krista.kell...@gmail.comwrote:
Thanks Allison,
So to be clear, I just need to rename
, 2013 at 8:47 PM, krista kelly krista.kell...@gmail.comwrote:
Also, just to add to this, if I rerun recon in 5.1 starting from the
normalization stage when I initially ran all subjects in 5.0, will this be
a problem?
On Wed, Oct 9, 2013 at 8:05 PM, krista kelly krista.kell...@gmail.comwrote
to
a ROI analysis with the atlases and labels, but I want to make sure that I
can trust the data that I have without having to rerun all of my
participants.
Thanks!
Krista
On Wed, Oct 9, 2013 at 9:15 PM, krista kelly krista.kell...@gmail.comwrote:
Hi again Allison,
After going through a few
To all my fellow Freesurfers...
Has anyone had any issues with doing recon-all on a Mac. I'm having a
problem with the automatically generated labels V1, V2, and MT (when loaded
in tksurfer there are holes in the mask) and I've been informed that this
may be an issue because of running the
Hello,
I'm running freesurfer's recon-all using Linux and the past few subjects
I've run, recon-all has exited with errors. I've ran a few subjects so far
with no problems, and now all of a sudden there's an issue and I can't
figure out why. I have been able to run these problem' subjects using
?
Thanks!
Krista
On Thu, Nov 14, 2013 at 10:48 AM, Alan Francis alandarkene...@gmail.comwrote:
Hi Krista:
You may want to update tcsh. You can do this by using SUDO and 'yum
update'.
best,
Alan
On Thu, Nov 14, 2013 at 10:42 AM, krista kelly
krista.kell...@gmail.comwrote:
Hello,
I'm
I'm using freesurfer v. 5.3 and I see a new annotation,
aparc.DKTatlas40.annot in the labels folder. Can anyone tell me what the
difference between this and the apart.annot is? Does it just have 40 labels
versus the 36 found in the older version?
Thanks!
Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in
the labels folder that every .label has a thresh.label. When overlaying the
two, they can be quite different (for example MT.label is much larger than
MT.thresh.label) or quite similar (V1.label is just a tiny bit larger
unlikely. The .thresh ones are
thresholded to pick the most likely vertices that give a label that is the
right surface area.
cheers
Bruce
On Sun, 17 Nov 2013, krista kelly wrote:
Hi, I've just started using the newest freesurfer v 5.3 and I've noticed
in
the labels folder that every .label
On Sun, 17 Nov 2013, krista kelly wrote:
Great thanks Bruce! I'm assuming then that using the thresh.label is the
best choice.
On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu
wrote:
Hi Krista
the unthresholded labels give every point that has
2013, krista kelly wrote:
Ok perfect. Just one last question, how would I use the thresholded option
for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009s.annot) when
doing whole brain analyses?
Thanks!
On Sun, Nov 17, 2013 at 1:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote
Hello,
I need to do a within group hemisphere comparison to see if there are any
hemisphere asymmetries in a patient group. I would like to do this in QDec
or if possible, somehow do it in freesurfer without using Qdec. I asked
this question two years ago and you mentioned that you were working
PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
yep, we have an existing stream complete with documentation and a
publication you can cite!
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 11/30/13 12:59 PM, krista kelly wrote:
Hello,
I need to do a within group hemisphere comparison
, krista kelly wrote:
Great thanks Douglas! I'm glad that this is available, I wasn't too keen
on using the 'flip the brain' method of looking for hemisphere asymmetries.
Just a few questions regarding the first step - Apply an existing atlas
(fsaverage_sym); this looks like a for loop, which I'm
Hi Gen,
I'm having the same problem right now with one participant where the pial
matter border doesn't extend enough out to the edge of the cortex. Did you
try adding control points as Ye suggested? If so, did it work?
Thanks!
Krista
On Tue, Sep 24, 2013 at 11:52 AM, ye tian
Hi,
I have one subject with a poor skull strip - much of the skull and neck are
left over. I have used one of the automated processes to remove the
problems areas and I now the skull strip is fine. If the talarairching,
pial and white matter borders, and labels were fine, do I need to rerun any
Hello,
I'm analysing interhemispheric differences using xhemi. I have followed the
instructions on the webpage with no problems. I do have a few questions
though.
1) When viewing the results in tksurfer, which color represents left
hemisphere is larger and which represents right hemisphere is
*(L+R))
Note that some people use
LI = (L-R)/(L+R)
If that is what you want, then divide the mris_preproc result by 2
doug
On 12/08/2013 08:45 PM, krista kelly wrote:
Hello,
I'm analysing interhemispheric differences using xhemi. I have
followed the instructions on the webpage
Great Thanks!
On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
On 12/09/2013 11:53 AM, krista kelly wrote:
Thanks Doug! I'll try that instead.
Also, do you or anyone else happen to have the answers to my other
questions (reposted below):
1) When
Hi,
I'm trying to run mris_anatomical_stats to get cortical thickness from
labels for each participant but I keep getting the following error:
MRISread: file '/Applications/freesurfer/subjects/MB19/surf/lh.thickness'
has many more faces than vertices!
Probably trying to use a scalar data file as
!
Krista
On Mon, Dec 9, 2013 at 4:00 PM, krista kelly krista.kell...@gmail.comwrote:
Great Thanks!
On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
On 12/09/2013 11:53 AM, krista kelly wrote:
Thanks Doug! I'll try that instead.
Also, do you or anyone
...@nmr.mgh.harvard.eduwrote:
Yes, use the cache files. When --cache is used, the csdbase=cache
On 12/10/2013 12:20 PM, krista kelly wrote:
Hi again,
I've looked into mri_glmfit-sim --help to figure out which files I
could overlay in tkurfer after correcting for multiple comparisons
using
, Dec 10, 2013 at 2:01 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Yes, use the cache files. When --cache is used, the csdbase=cache
On 12/10/2013 12:20 PM, krista kelly wrote:
Hi again,
I've looked into mri_glmfit-sim --help to figure out which files I
could overlay in tkurfer
is based on comparisons of actual and predicted V1 boundary with an
independent dataset.
Relevant pub: https://surfer.nmr.mgh.harvard.edu/ftp/articles/
hinds2008accurate.pdf
-Louis
On Thu, 16 Jan 2014, krista kelly wrote:
Hi all,
Can anyone provide information regarding how v1.thresh.label
, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
yes, it is just like a normal group analysis. You create a stack of LI
maps, one for each subject, create an FSGD file, run mri_glmfit, then
mri_glmfit-sim.
doug
On 01/13/2014 06:22 PM, krista kelly wrote:
Just wanted to repost
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 (
PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
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
Hello,
I followed instructions on how to incorporate the lgi_pial measure into
QDec, however, it's not coming up when I go to choose this as a measure. I
ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a
Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight
named
?h.pial_lgi.fwhm?.fsaverage.mgh in the surf folder of one of your subject
if you want to be sure.
Let me know,
Marie
On Feb 25, 2014, at 6:55 PM, krista kelly krista.kell...@gmail.com
wrote:
Hi Marie,
I have tried adding the .Qdecrc file into the home folder as well
lines.
Then start qdec again, it should work. If not, check again the .Qdecrc
file, and look whether starting qdec erases the added line.
Let me know,
Marie
On Feb 28, 2014, at 1:09 PM, krista kelly krista.kell...@gmail.com
wrote:
Hi Marie,
The ?h.pial_lgi.fwhm?.fsaverage.mgh files
to see whether
opening qdec had any effect on the line that you added (by running the
command more ~/.Qdecrc before and after opening qdec)?
I need you to explain me a bit more how you did, otherwise it's
difficult for me to help you.
Marie
On Mar 4, 2014, at 5:20 PM, krista kelly
Hello,
I would like to extract the pial_lgi data from Freesurfer's V1.thresh
labels but can't quite figure it out. I've tried adapting the commands from
the LGI Freesurfer tutorial as such:
mri_segstats --label-thresh BV20 lh V1.thresh.label --i
$SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum
.thresh.label.stats
On 03/05/2014 11:15 AM, krista kelly wrote:
Hello,
I would like to extract the pial_lgi data from Freesurfer's V1.thresh
labels but can't quite figure it out. I've tried adapting the commands
from the LGI Freesurfer tutorial as such:
mri_segstats --label-thresh BV20 lh V1
Perfect, it works thanks!
On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
sorry, it is --slabel
btw, there is documentation. If you run it without options it gives you a
list of arguments as well as examples
doug
On 03/05/2014 11:32 AM, krista kelly wrote
, 2014 at 1:21 PM, krista kelly krista.kell...@gmail.comwrote:
Perfect, it works thanks!
On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
sorry, it is --slabel
btw, there is documentation. If you run it without options it gives you a
list of arguments
On 03/05/2014 01:42 PM, krista kelly wrote:
Hi again,
My apologies for the barrage of emails! I was able to do mri_segstats on
V1 labels for pial_lgi using the following:
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
$SUBJECTS_DIR/$s/surf
miss places where
V1 is the most likely but still less than .5. I would probably use
lh.V1.thresh.label (and then do not spec --label-thresh)
doug
On 03/05/2014 03:40 PM, krista kelly wrote:
Thanks Doug! I did that and it worked, but now here's another problem:
the values that I obtained
Does anyone know of any support (i.e. articles/data) suggesting that the V1
and V2 labels automatically created in the Freesurfer pipeline, especially
when looking at surface area/gyrification, are valid to use with clinical
populations? In particular, visually deprived populations?
Thanks!
think we have any idea. The labels are based purely on anatomy, but
whether those areas keep their functional specification we have no idea.
let us know if you find out though!
Bruce
On Wed, 18 Jun 2014, krista kelly wrote:
Does anyone know of any support (i.e. articles/data) suggesting
Hi all,
I'm trying to extract cortical thickness data from each lobe per
participant. Here are the commands I used so far:
1) create annotation file for lobes: mri_annotation2label --subject $s
--hemi lh --lobesStrict lh.lobesStrict.annot
2) extract lobe labels: mri_annotation2label --subject
Hello,
I need to download an older version of freesurfer (Version 5.0) on a Mac
Lion 10.7.5. In the archives I don't see a file for Lion, just Leopard and
Tiger. Is it possible that either of these will work for Lion? Also, are
there any step by step instructions on how to install?
Thanks!
Hello,
Is there any way to find out which Freesurfer version I used to process
data?
Thanks,
Krista
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The information in this e-mail
I'm using the labels saved in QDEC to extract cortical thickness values for
certain regions. For example, I've used the lh.v1.label to map onto the
fsaverage brain and then to map this onto each individual subject. When I
load the lh.PALS_B12_Brodmann.annot or the lh.PALS_B12_Visuotopic.annot onto
Hi, just wondering if anyone has any advice on the following questions:
I'm using QDEC to analyze cortical thickness differences between groups and
I have a few questions:
1) There are a few variables that I need to control for. First variable is
scanner - I used two different scanners of
When I extract surface area data using the following commands, which
measure of surface area am I getting, the pial surface, the WM surface, or
the total of both combined?
aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh --meas area
--tablefile aparc_stats_rh.txt
Thanks!
Krista
I'm looking at both cortical thickness and surface area differences between
two groups. I've been using mris_anatomical_stats to retrieve values but had
a few questions:
1) Do I need to do separate mris_anatomical_stats using different thickness
files (bolded below) to get cortical thickness and
I'm using QDEC to analyze cortical thickness of a patient population
compared to controls. One of the things I wanted to analyze is the
difference between hemispheres within patients. It seems that I can only
analyze one hemisphere at a time in QDEC; is there any way to analyze the
difference
Using QDec, I've created an ROI label (lh.G_cuneus.label) and a .stats
file (lh.G_cuneus.stats) that corresponds to this ROI for each participant
in my group. Is there a quick way to compile cortical thickness data for
this ROI from all participants? The manual suggests using aparcstats2table
but
How do I stop receiving emails from everyone asking and responding to
questions about FreeSurfer?
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The information in this e-mail is
: krista kelly krista.kell...@gmail.com
Date: Wed, Jun 18, 2014 at 4:51 PM
Subject: Re: [Freesurfer] V1 and V2 labels valid with clinical populations?
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
OK thanks. I see a lot of pubs using these labels. Can anyone provide any
advice on how
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