: krista kelly
Date: Wed, Jun 18, 2014 at 4:51 PM
Subject: Re: [Freesurfer] V1 and V2 labels valid with clinical populations?
To: Freesurfer support list
OK thanks. I see a lot of pubs using these labels. Can anyone provide any
advice on how to justify using these labels in clinical populations
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 $s
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. a
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!
Krista
ou may 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
how all values are the same for each label for all participants (V1,
V2, cortex.LGI.txt).
If anyone has any insight into the problem, that would be great!
Best,
Krista
On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve
wrote:
>
> use asegstats2table (I know, it's confusing:)
> dou
ps.
Thanks!
Krista
On Wed, Mar 5, 2014 at 1:21 PM, krista kelly wrote:
> 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 yo
Perfect, it works thanks!
On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
wrote:
> 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
ts
>
> 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 t
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 lh.V1.thr
e? Did you check 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
dd it, I have it before all the Qdec
> 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
> wrote:
>
ly (you can check that you have some files 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
> wrote:
>
> Hi Marie,
>
> I have t
menu of qdec, look at the following post:
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html
>
> Otherwise can you describe more precisely the issue?
>
> Best,
>
> Marie
>
> On Feb 24, 2014, at 1:21 PM, krista kelly
> wrote:
>
> >
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 a
3, 2014 at 2:02 PM, Douglas N Greve
wrote:
> 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 anal
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 (
ht
, Douglas N Greve
wrote:
>
> 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:
> >
reshold
> 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,
Hi all,
Can anyone provide information regarding how v1.thresh.label and
v2.thresh.label that are automatically implemented in FreeSurfer are
thresholded?
Thanks!
Krista
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n Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve
wrote:
>
> 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
t;
> 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
ssible?
Thanks!
Krista
On Mon, Dec 9, 2013 at 4:00 PM, krista kelly wrote:
> 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:
>> > Th
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
Great Thanks!
On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve
wrote:
>
> 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
= (L-R)/(.5*(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 differenc
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
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
of
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 wrote:
> Dear Ge
Great thanks! I'll try that. I've also figured out that I can just add the
subjects into the brackets that say subject list. But I'll try your method
just in case I'm wrong. Thanks again!
On Tue, Dec 3, 2013 at 11:26 PM, Douglas Greve wrote:
>
> On 12/3/13 11
Thanks again!
On Sat, Nov 30, 2013 at 2:34 PM, Douglas Greve wrote:
>
> 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 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 on
Ok great! Thanks for the quick responses, and for your help.
Best,
Krista
On Sun, Nov 17, 2013 at 1:26 PM, Bruce Fischl wrote:
> no, those are whole-brain parcellations so ever vertex is already assigned
> the most likely label for it
>
>
> cheers
> Bruce
> On Sun, 17 N
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
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 noti
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 th
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!
___
doing it wrong?
Thanks!
Krista
On Thu, Nov 14, 2013 at 10:48 AM, Alan Francis wrote:
> 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
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
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 program
brain analyses prior 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 wrote:
> Hi again Allison,
>
> After going throu
Oct 9, 2013 at 8:47 PM, krista kelly wrote:
> 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 wrote:
>
&
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 wrote:
> Thanks Allison,
>
> So to be clear, I just need to rename talairach.au
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
bject 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 pict
hat too much.
Thanks!
On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve
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 are
editing can take away from the standardization of the process and I
wouldn't want to mess with that too much.
Thanks!
On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve
wrote:
>
> How did you do the transfer? What was your cmd line?
> doug
>
> On 09/10/2013 05:31 PM, krista kelly
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 woul
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
Hello,
Is there any way to find out which Freesurfer version I used to process
data?
Thanks,
Krista
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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!
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 s
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
_
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 differe
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
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 different field strengths (1.5T
GE and 3T Siemens) so I wanted to control for sc
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 i
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 I
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 I
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 BETWE
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