Dear FreeSurfers,
I have a ROI that I want to correct with FDR. I found that FreeSurfer has
different implementations of FDR correction and all of them give different
results.
My ROI has 4205 vertices with p values between -5.0366 and 1.1673.
When I set FDR in tksurfer (MRISfdr2vwth), I get p
e problem is
> that you then end up with stuff outside of the ROI smoothing into the
> ROI. Also note that either way, you will need to generate new tables for
> correction of multiple comparisons (use use permutation)
>
>
> On 03/15/2017 03:52 PM, Mihaela Stefan wrote:
>
;gr...@nmr.mgh.harvard.edu>
wrote:
> yes, that is the right way to do it
>
>
> On 03/15/2017 01:18 PM, Mihaela Stefan wrote:
> > Hello FreeSurfers,
> >
> > I would like to run a group analysis on cortical thickness using
> > existing Desikan labels.
> >
> >
Hello FreeSurfers,
I would like to run a group analysis on cortical thickness using existing
Desikan labels.
When I run the command for smoothing, should I replace *--cortex* with
*--label-trg*? In other words, for ROI analysis, should we smooth *only*
the target mask?
mri_surf2surf --hemi lh \
Hello FreeSurfers,
I am trying to run recon-all -s -localGI on a longitudinal dataset
but I get this error:
ERROR: Are you trying to run or re-run a longitudinal time point?
If so, please specify the following parameters:
\' -long \'
where is the time point id (SAME as
Hello FreeSurfers,
I am trying to run recon-all -s -localGI on a longitudinal dataset
but I get this error:
ERROR: Are you trying to run or re-run a longitudinal time point?
If so, please specify the following parameters:
\' -long \'
where is the time point id (SAME as
Hello FreeSurfers,
I successfully ran the command recon-all -s -localGI for one of my
subjects. However, the resulted ?h.pial_lgi files don't look right to me. I
am attaching a pic for the right hemi (I made sure the overlay is
rh.pial_lgi).
Can someone help me figure out what went wrong?
;gr...@nmr.mgh.harvard.edu>
wrote:
> What do you mean a "plot"? I had assumed you wanted to average over
> clusters, but FDR does not produce clusters
>
>
> On 11/07/2016 04:26 PM, Mihaela Stefan wrote:
> > That seems to be for Monte Carlo simulation. What if I use FDR or
--glmdir and
> setting the thresholds and signs as you had them in qdec. The output
> will then be in a file called something like cache.th20.pos.y.ocn.dat.
> the cluster summary table will be in cache.th20.pos.sig.cluster.summary
>
>
> On 11/07/2016 12:33 PM, Mihaela Stefan wrote:
> >
Hello Freesurfers,
I am doing a group analysis using Qdec. I have a few significant clusters
and I would like to plot one of them. Qdec does that if I click on 'Find
Clusters and Goto Max' but I don't see options for the design of the plot.
How can I export the thickness values from my cluster to
you need to add --surface fsaverage lh to the mri_glmfit command
> line, otherwise it thinks it is a volume-based analysis
>
> On 07/22/2016 01:58 PM, Mihaela Stefan wrote:
> > It's surface-based analysis.
> >
> > On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve
>
It's surface-based analysis.
On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> Are you doing volume or surface-based analysis? If volume, then you'll
> need a volume mask and the --label is not appropriate.
>
> On 07/22/2016 01:36 PM, Mi
> On 07/22/2016 10:38 AM, Mihaela Stefan wrote:
> > Hi Doug,
> >
> > I used this command:
> > mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 1018 1020
> > 1019 --i aparc+aseg.mgz --o lh22mask.mgz
> >
> > When I checked it first time, I o
Hello freesurfers,
I would like to use mri_glmfit with --mask but I get this error: dimension
mismatch 1 between y and mask.
I created a binary mask from 22 aparc labels (using mri_binarize) and I
would like to run a surface-based analysis only on those regions. The
command I use is:
mri_glmfit
Hello Freesurfers,
What is the command line to load the control.dat file (control points) in
freeview? We tried -cp but it didn't work.
Thanks!
Mihaela
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Freesurfer@nmr.mgh.harvard.edu
> On Wed, 13 Jul
> 2016, Mihaela Stefan wrote:
>
> > Hello Freesurfers,
> >
> > We would like to know how to calculate the total pial surface area for
> each hemisphere. We extracted the surface area from the 34 ROIs per hemi
> from
> > lh.aparc.stats but there i
Hello Freesurfers,
We would like to know how to calculate the total pial surface area for each
hemisphere. We extracted the surface area from the 34 ROIs per hemi from
lh.aparc.stats but there is no total pial surface area in that file (only
white surface area).
Does it make sense to just add the
*The Cognitive Development and Neuroimaging Lab* in the *Division of Child
and Adolescent Psychiatry in the Department of Psychiatry, Columbia
University Medical Center and the New York State Psychiatric Institute*
invites applications for a post-doctoral associate in the area of
developmental
gt; addition to a T1 (FLAIR, T2SPACE, T2*)
>
> cheers
> Bruce
>
>
>
> On Tue, 19 Apr 2016, Mihaela Stefan wrote:
>
> Dear Freesurfers,
>> We noticed that some subjects in our study have the average cortical
>> thickness values in entorhinal and temporal pole above
Dear Freesurfers,
We noticed that some subjects in our study have the average cortical
thickness values in entorhinal and temporal pole above 4 mm. They are
adolescent girls so they're pretty young but we wonder if these values are
accurate. Visually, their segmentations seem good.
In an older
Hi Martin,
I am reposting this. Should we include the missing baseline in the qdec
table or leave it out?
Thanks!
Mihaela
On Wed, Apr 13, 2016 at 8:30 AM, Mihaela Stefan <mikaelastep...@gmail.com>
wrote:
> Hi Martin!
> Sorry to bug you but I have one more question. How do I cre
rd.edu>
wrote:
> It does not compute this. Often people use time-from-baseline for their
> analysis and control for age (@ baseline).
> Best Martin
> On Apr 12, 2016 6:23 PM, Mihaela Stefan <mikaelastep...@gmail.com> wrote:
>
> Thanks Martin!
>
> Related to the longitu
inal image processing pipeline does not care which one is
> baseline and which are follow ups. It only cares what images belong to the
> same subject.
> So, yes you can process this one with only two tone points instead of
> three.
>
> Best Martin
> On Apr 12, 2016 5:09 PM, Miha
Hello FreeSurfers,
We are conducting a longitudinal analysis and we have a subject who is
missing the structural at baseline (it has fMRI data though). That subject
returned for the 1st and the 2nd follow-up. Can we process the longitudinal
pipeline the usual way and account for the missing
d/wachinger-brainprint15
> http://reuter.mit.edu/software/brainprint/
>
> Best, Martin
>
>
>
> On 04/05/2016 12:49 PM, Mihaela Stefan wrote:
>
> Hi Martin,
> Just an update on this. It turned out that there was just a DICOM mismatch
> for this subject but now that
length of
the study, it's quite difficult for that person to remember hundred of
faces and asking for an ID is not always doable.
Thanks!
Mihaela
On Thu, Mar 31, 2016 at 1:50 PM, Mihaela Stefan <mikaelastep...@gmail.com>
wrote:
> Wow! I haven't thought about that but it's possible since we
n't have
> time to come to the follow up themselves, has also happened - not to me
> though ).
>
> Best, Martin
>
>
> On 03/31/2016 10:21 AM, Mihaela Stefan wrote:
>
> Hi Martin,
>
> We ran this subject twice but we got the same error. The norm is not
> aligned. T
itudinal directory first so that it re-runs from
> scratch. If that does not fix it, we would need to get the data for
> debugging.
>
> Thanks, Martin
>
>
> On 03/30/2016 03:19 PM, Mihaela Stefan wrote:
>
> Dear FreeSurfers,
>
> We are doing a longitudinal analysis w
It worked in tksurfer!
Thanks!
Mihaela
On Tue, Jan 5, 2016 at 1:13 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> How does it look in tksurfer?
>
> On 01/04/2016 03:29 PM, Mihaela Stefan wrote:
> > Hi Doug,
> >
> > I am going back to this old email.
nd.
>
>
> On 10/27/2015 02:35 PM, Mihaela Stefan wrote:
> > Hello Freesurfers,
> >
> > I would like to be able to display just a few parcels from the Desikan
> > atlas on the fsaverage inflated surface. For example, I would like to
> > display only t
of those clusters will have a p-value,
they just choose not to report them.
doug
On 5/29/15 11:50 AM, Mihaela Stefan wrote:
Hi Doug,
The simulation went smoothly, however, as I suspected, no clusters were
detected. I wonder if you have any thoughts about my question in the
previous email
Hi Doug,
The simulation went smoothly, however, as I suspected, no clusters were
detected. I wonder if you have any thoughts about my question in the
previous email, regarding the uncorrected p values.
Thanks!
Mihaela
On Thu, May 28, 2015 at 11:09 AM, Mihaela Stefan mikaelastep...@gmail.com
, Mihaela Stefan wrote:
Thanks! It seems that there was a white space. I ran the permutation
command but now I got another error:
ERROR: design matrix is not orthogonal, cannot be used with permutation.
If this something you really want to do, run with --perm-force
Wed May 27 16:27:50 EDT 2015
Dear Martin,
I'm pitching in since this topic concerns me as well.
We are collecting structural data for a longitudinal study with
adolescents. The youngest is 13 years old at baseline and the mean age is
around 16. We will collect 3 follow-ups with a gap of 1.5 - 2 years. The
adolescent brain is
in the base by computing the union, but that may be too
large for some earlier time points, so you may have to edit them in the
long etc.).
Best, Martin
On 05/28/2015 11:54 AM, Mihaela Stefan wrote:
Dear Martin,
I'm pitching in since this topic concerns me as well.
We are collecting
run it with --debug as the first option?
On 05/27/2015 03:39 PM, Mihaela Stefan wrote:
Hello FreeSurfers,
I am trying to run a clusterwise correction following this link:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
I would like to use the permutation simulation
Dear FreeSurfers,
I use FS v5.3 on Ubuntu 12.04.3 LTS. I am working on a longitudinal study
and now I have problems with my machine. It started to work very slowly and
it's losing the Internet connection frequently without apparent reason. I
believe there's a bug that affects its performance
Thanks!
Mihaela
On Wed, Apr 8, 2015 at 12:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
that should be fine
Bruce
On Wed, 8 Apr 2015, Mihaela Stefan wrote:
Dear FreeSurfers,
I use FS v5.3 on Ubuntu 12.04.3 LTS. I am working on a longitudinal study
and now I have problems
Thank you for clarifying this.
Mihaela
On Tue, Nov 25, 2014 at 11:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
No, I don't think so
Bruce
On Nov 25, 2014, at 11:05 PM, Mihaela Stefan mikaelastep...@gmail.com
wrote:
Hi Bruce,
I've heard people saying that FS 5.3 is focusing
Hi Bruce,
I uploaded a subject.
Thanks!
Mihaela
On Tue, Nov 25, 2014 at 10:13 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Mihaela
if you want to upload a representative subject we will take a look
cheers
Bruce
On Tue,
25 Nov 2014, Mihaela Stefan wrote:
Hello Freesurfers
Hi Bruce,
I've heard people saying that FS 5.3 is focusing on better output for
cortical thickness and that I should use 5.0 for subcortical segmentation
because it's better. Does that make sense?
Thanks!
Mihaela
On Tue, Nov 25, 2014 at 10:43 AM, Mihaela Stefan mikaelastep...@gmail.com
wrote
Hi Freesurfers,
I would like to use in my analysis the volumetric measures for the dorsal
putamen. The aseg.stats file generated during recan-all outputs the volume
for the whole putamen. I think I will have to manually draw myself a volume
of interest including the dorsal putamen. What is the
Hello,
I am re-posting this since I haven't got an answer yet.
Thanks!
Mihaela
On Fri, Feb 21, 2014 at 3:55 PM, Mihaela Stefan mikaelastep...@gmail.comwrote:
Hi freesurfers,
I get this error when I load qdec.table.dat. Is it something wrong or
should I ignore it?
Verifying subject data.sh
...@gmail.com wrote:
Please be sure to 'reply all' so everyone may participate.
Yes, You need to set the SUBJECTS_DIR before using freesurfer tools.
HTH
D
On Tue, Mar 4, 2014 at 2:02 PM, Mihaela Stefan mikaelastep...@gmail.com
wrote:
It says No such file or directory
The environment
Hi freesurfers,
I get this error when I load qdec.table.dat. Is it something wrong or
should I ignore it?
Verifying subject data.sh: 1: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject '6027' in
SUBJECTS_DIR
.sh: 1: Syntax error: Bad fd number
ERROR:
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 thistutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnal
ysis_freeview
I
?
Thanks!
Mihaela
On Fri, Jan 24, 2014 at 8:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
it's possible that the timestamps on your system are wrong I guess. Did
-make all run anything?
On Fri, 24 Jan 2014, Mihaela Stefan wrote:
Hi Bruce,
I used that command and I got the same
Hi Louis,
I've got the idea about the wm edits, but I have a related question. From
what I see, that's a coronal cut at the level of the amygdala basal
ganglia. Isn't that the gray area? How relevant is to make edits in that
area?
Thanks!
Mihaela
On Thu, Sep 19, 2013 at 4:07 PM, Louis
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