-7OR0ZajBrz3jJMaAXx2tGeFbJuIT_cwpTPX2u7uVcKu40byzK3CksUD9sBXUODMzo1dWFYJ7dqv9jzjPyhXiM51d49k7iGamx_SlWvcrdjka0R328JXdXbqwiXqt2FEwAVsz1ioBdFbSPNdth73sqgmm1hDt5vQsBMMp8Txr8bGJeZxE6q-ZHf8yqwxiFsXOOVtBw/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC9724189%2F).
On Fri, Feb 23, 2024 at 10:27 AM Douglas N. Greve
wrote:
> Sorry, don't know what VLSM is. Can you elaborate?
>
> On 2/6/2024 3:19 PM, Martin Juneja wrote:
>
>
External Email - Use Caution
Dear Juan and FreeSurfer developers,
I am trying to run the *mri_synthsr *command on a MacPro M2 Max chip (OS
13.6.4) - but somehow, I am getting the following error when I try to run
this command. I am using FreeSurfer's 7.4.1 version.
*Illegal
External Email - Use Caution
Dear FreeSurfer community and experts,
I would greatly appreciate any help/response with the following.
Thanks.
-- Forwarded message -
From: Martin Juneja
Date: Wed, Jan 31, 2024 at 7:51 PM
Subject: Vertex / voxel lesion symptom
External Email - Use Caution
Greetings FreeSurfer community,
I was just wondering if it's possible to perform vertex/voxel lesion
symptom mapping (VLSM) using FreeSurfer? In other words, I would like to
assess the impact of lesion topography (of course, heterogenous locations
External Email - Use Caution
Hi FS experts,
I was wondering if someone could help me get the following issue resolved.
Thanks.
-- Forwarded message -
From: Martin Juneja
Date: Fri, Dec 8, 2023 at 11:03 AM
Subject: Case-controls study !
To: Freesurfer support
External Email - Use Caution
Hello FreeSurfer experts,
In my case-control study, I have a dataset of 5 healthy controls (HCs) and
one patient (PAT). I was wondering if there is any way to perform GLM for
PAT > HCs on brain morphometry data.
When I tried to follow instructions
External Email - Use Caution
Hi FreeSurfer experts,
We submitted a paper where we used Yeo's 7-network atlas to estimate the
hemispheric mean cortical volume of each network using mri_annotation2label
--subject X --hemi lh --annotation Yeo2011_7Networks_N1000 --labelbase
Left_7Ns
External Email - Use Caution
Dear Thomas and FreeSurfer experts,
Here I am just reposting my question below - just in case this was missed
by the experts. Any help would be really appreciated.
-- Forwarded message -
From: Martin Juneja
Date: Sat, Jul 10, 2021
tional atlas where the default network is well defined. If you use a
> structural atlas like the Desikan-Kiliany atlas, then you will still need
> to use a functional atlas to roughly assign the Desikan-Kiliany parcels to
> the default network, which does not seem that great either.
>
>
External Email - Use Caution
Hi all,
I am reposting my concerns below. I would really appreciate any help.
-- Forwarded message -
From: Martin Juneja
Date: Fri, Jun 18, 2021 at 6:16 PM
Subject: Yeo atlas for children!
To: Freesurfer support list
Dear experts
External Email - Use Caution
Dear experts,
I used Yeo's 17-network parcellation to study the association between
network-wise cortical volume and a clinical variable in adolescents. I
received the following two questions from the reviewers regarding the use
of Yeo's atlas. I
is the
correct flag here?
Thanks.
On Wed, Sep 30, 2020 at 1:04 PM Martin Juneja wrote:
> Dear Doug,
>
> Yes, that gives me subjectwise values if I run the following command, but
> now the output doesn't seem to be the volume values, it gives very small
> subjectwise valu
PM Douglas N. Greve
wrote:
> Use the --avgwf output.table instead of --sum
>
> On 9/30/2020 1:48 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Dear Doug,
>
> Thanks for your response. I created a binary mask and ran the following
> command, but t
(eg, created by
> mris_preproc)
>
>
> On 9/29/2020 1:32 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Dear Doug and FreeSurfer team,
>
> Any help with this on an urgent basis would be really appreciated. Sorry
> for being a little impatient :(.
>
External Email - Use Caution
Dear Doug and FreeSurfer team,
Any help with this on an urgent basis would be really appreciated. Sorry
for being a little impatient :(.
Thank you so much !
-- Forwarded message -
From: Martin Juneja
Date: Mon, Sep 28, 2020 at 5:42
External Email - Use Caution
Hello everyone,
I have significant group differences in volume (controls > patients) for
one of the clusters (say C1) - calculated after permutation test using
PALM, which gives me following outputs:
*_clustere_tstat_fwep.mgz (this is significant at
External Email - Use Caution
Hello FreeSurfer experts,
I have this interesting situation. I understand its important to include
ICV as a covariate while conducting cortical volume (CV) analysis.
So for my clinical sample (CL) vs healthy-controls (HCs):
1. If I do *network-wise*
On 7/14/2020 5:00 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Hi experts,
>
> I extracted network-wise cortical measures (i.e., 7 cortical thickness
> values for 7 networks for Yeo atlas).
>
> I was wondering if there is a way to get the
External Email - Use Caution
Hi FreeSurfer experts,
I am trying to run write_annonation program in MATLAB and getting following
error:
>> [v, L, ct] = read_annotation('lh.Yeo2011_7Networks_N1000.annot');
>> ct.table(1:6,1:3) = 1;
>> write_annotation('lh_Yeo2011_DMN',v,L,ct);
External Email - Use Caution
Hi experts,
I extracted network-wise cortical measures (i.e., 7 cortical thickness
values for 7 networks for Yeo atlas).
I was wondering if there is a way to get the cortical thickness of each ROI
within each of these networks e.g., cortical
at 9:13 AM Douglas N. Greve
wrote:
>
>
> On 6/29/2020 8:45 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Hello experts,
>
> I am following these instructions
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis to
> anal
External Email - Use Caution
Hello experts,
I am following these instructions
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis to
analyze the association between IQ and whole brain cortical thickness of
brain areas (which by default uses Desikan atlas of 34
rry, I'm not sure I'm following. It looks like you did two analyses, one
> with 10mm smoothing and CFT=.05, the other with 12mm and CFT=.001. You get
> a cluster for each in the same area, but they are not overlapping. Is that
> right?
>
> On 1/6/2020 2:58 PM, Martin Juneja wrote:
>
-6733.96 middletemporal
2 -4.531 110270 1924.64-17.2 57.8 -13.3 0.00020 0.0
0.00040 3444-6888.13 rostralmiddlefrontal
On Mon, Jan 6, 2020 at 2:58 PM Martin Juneja wrote:
> Hi,
>
> I am using Monte-Carlo simulations (for cortical thickness a
isn't that true that if I use -C 1.95 in addition to the flag twotail
- this will apply two-tailed twice?
Also, I was wondering how can I apply Bonf. Corr. for two hemispheres in
the above command, or by-default this is already applied?
Thanks.
On Tue, Jan 7, 2020 at 12:30 PM Martin Juneja wrote:
External Email - Use Caution
Hi,
I am trying to run PALM in MATLAB. After I run the following command, I get
following error:
palm -i SPSX/lh.SPS_vol.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d
SPSX/lh.SPS_vol.glmdir/X.mat -t Corr-SPS-cor.csv -m
External Email - Use Caution
Hi,
I am using Monte-Carlo simulations (for cortical thickness and volume -
behavioral analysis) for clusterwise correction for multiple comparisons.
My results are either significant at (i) CFT < 0.001 and CWT < 0.1 (i.e.,
CWT = 0.07) (smoothing 12
: matrix is ill-conditioned or badly scaled, condno = 385372
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
Thanks.
On Fri, May 24, 2019 at 9:42 AM Martin Juneja wrote:
>
External Email - Use Caution
Hi Dough,
Please find the Xg.dat file attached here.
Thanks.
On Fri, May 24, 2019 at 7:30 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Can you send the Xg.dat file?
>
> On 5/23/2019 8:43 PM, Mart
External Email - Use Caution
Hi FS experts,
I want to find clusters showing an association between cortical measures
and behavior x6 (sex, age and variables x1-x5 as covariates).
My FSGD file looks like:
GroupDescriptorFile 1
Class Male
Class Female
Variables x1 x2 x3 x4 x5 x6
; I would run recon-all on the MNI152, then sample the ROIs onto the
> MNI152 surface, then transfer them to fsaverage using mris_apply_reg or
> mri_surf2surf.
>
> On 5/15/19 1:46 PM, Martin Juneja wrote:
> >
> > External Email - Use Caution
> >
> > Hi FS e
preserve the thickness (unless you are using a head-only
> system, which you are not)
>
> On Tue, 14 May 2019, Martin Juneja wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you so much Martin, Matthew and Bruce for all the detailed
&g
or to running FS. That is why Matthew asked
> > what MRI data was collected exactly (sequence, scanner etc).
> >
> > Best, Martin
> >
> > On Mon, 2019-05-13 at 21:06 -0700, Martin Juneja wrote:
> >> External Email - Use Caution
> >> Thank you Matthe
your data to
> differing extents. What kind of MRI data was in your study?
>
> Matt.
>
>
>
> *From: * on behalf of Martin
> Juneja
> *Reply-To: *Freesurfer support list
> *Date: *Monday, May 13, 2019 at 6:53 PM
> *To: *Freesurfer support list
> *Subject: *[Freesurfer] G
External Email - Use Caution
Hi experts,
I have following question from one of the reviewers regarding recon-all
pipeline:
*"Was geometric distortion corrected? If not, this should be discussed or
mentioned in the study limitation."*
I was wondering if the reviewer is referring
External Email - Use Caution
Never mind, I just got it working by replacing "white.H" with "meancurv".
Thanks.
On Wed, Jan 16, 2019 at 5:32 PM Martin Juneja wrote:
> Hi Freesurfer experts,
>
> I am interested in estimating mean curvature index
External Email - Use Caution
Hi Freesurfer experts,
I am interested in estimating mean curvature index for each of the 7
networks (Yeo7 atlas) for my data of healthy controls. I am able to
estimate this subjectwise, and the output stats file for each subject looks
like following:
t; curvature implies smaller r (and sharper folds).
>
> As for you question (2), I think that is a biological one and depends on
> the effect you are looking for (unless I am misunderstanding)
>
> cheers
> Bruce
>
>
> On
> Thu, 20 Dec 2018, Martin Juneja wrote:
>
> &g
ll leave that up to Bruce and Rudolph
> >
> > On 12/19/2018 05:37 PM, Martin Juneja wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Thanks Dr. Greve. That works, but both white.K and white.H are giving
> >> me very different output
dgr...@mgh.harvard.edu> wrote:
> something like --meas white.K or white.H
>
>
> On 12/19/2018 04:23 PM, Martin Juneja wrote:
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > Just like volume, I have "Folding Index" measures sav
External Email - Use Caution
Hi,
Just like volume, I have "Folding Index" measures saved in
lh/rh.aparc.stats files for each subject.
If I am using mris_preproc *--meas volume* --out CV/lh.CV.mgh command to
concat cortical volume files from all subjects, then how can I use this
ll the clusters regardless of significance, run it
> with a CWT of 1. If you want to run with a more liberal cluster forming
> threshold (CFT), you can try using permutation. See
> http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>
> On 12/05/2018
External Email - Use Caution
Dear experts,
Could you please help me in resolving following issue?
Thanks.
-- Forwarded message -
From: Martin Juneja
Date: Wed, Nov 28, 2018 at 2:23 PM
Subject: Overall maxima is high and still no significant cluster
External Email - Use Caution
Hi FS experts,
I am estimating the group-behavioral thickness interaction using contrast 2
FSGD file: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT <
0.01 and CWT < 0.05 at FWHM of 12 mm.
I do not find any significant clusters and my
External Email - Use Caution
Hello FS experts,
I am using longitudinal processing pipeline (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) to
calculate the cortical volume (CV) over a course of treatment (two
conditions: pre condition and post condition). In
External Email - Use Caution
Hi,
I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
version of FreeSurfer.
I used cross-sectional pipeline to identify ROIs (from Desikan atlas) with
significant difference in cortical volume (CV) between controls and *patients
External Email - Use Caution
Hi FS experts,
I came across this post
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031245.html
by Dr. Bruce Fischl, where it is mentioned that "*You won't be able to
analyze the data unless **it is T1-weighted with voxels that are
bject in the stack,
> the value will be the mean in cluster N
>
>
> On 8/13/18 11:48 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> For instance, if there is any way to extract spatial location of cluster
> X1 and use this location to extract thickness values of al
, then how can we do that?
On Mon, Aug 13, 2018 at 7:04 PM, Martin Juneja wrote:
> Hi experts,
>
> I found a cluster X1, which showed significant difference in cortical
> thickness between two groups C1 and P1, determined
> using mris_preproc, mri_surf2surf and mri_glmfit commands.
>
External Email - Use Caution
Hi experts,
I found a cluster X1, which showed significant difference in cortical
thickness between two groups C1 and P1, determined
using mris_preproc, mri_surf2surf and mri_glmfit commands.
I am interested in determining if the same cluster X1 has
red effect as seen the
> in gamma. Sorry, I don't know what else to tell you.
>
>
>
> On 7/26/18 1:24 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Dear Dr. Greve,
>
> I am so sorry for annoying you with multiple emails.
> I clearly got the differen
Not sure what you want me to comment on.
>
>
>
> On 7/24/18 2:17 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Just to add some more info here:
> The peak location of regions, X1 and X2, which I found without including
> ICV as covariate are very c
(range -0.6 to
+0.6).
I am not sure if this additional info adds anything to interpret gamma.mgh
with and without ICV as covariate.
On Tue, Jul 24, 2018 at 10:10 AM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> So I checked both. The rstd.mgh files are very similar in both cases (with
>
happened.
>
>
> On 7/23/18 8:30 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Hello experts,
>
> I am interested in identifying regions of interest by comparing cortical
> volume (CV) between controls and patients.
>
> After including age and sex as my co
External Email - Use Caution
Hello experts,
I am interested in identifying regions of interest by comparing cortical
volume (CV) between controls and patients.
After including age and sex as my covariates, I identified regions X1 and
X2, which showed significantly lower CV for
. for following fsgd:
Class Male
Class Female
Variables *Perform*Age*
Input S1 Male 180
Input S2 Female 167
Thanks.
On Mon, Feb 26, 2018 at 2:31 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
>
> On 02/24/2018 12:00 AM, Martin Juneja wrote:
> > Hi experts,
> >
&g
Hi experts,
I am not sure if this has already been addressed in FS discussion.
If my fsgd file looks like following:
Class Male
Class Female
Variables Performance Age
Input S1 Male 181 25
Input S2 Female 167 23
I understand that the contrast matrix *[**0 0 1 -1 0 0]* represents
at 3:18 PM, Martin Juneja <mj70...@gmail.com> wrote:
> Hi FS experts,
>
> I have two population groups X1 (controls) and X2 (patients). I am
> interested in calculating impact of sex (F or M) on causing difference
> between both groups e.g. I am interested in following 4 contr
Hi FS experts,
I have two population groups X1 (controls) and X2 (patients). I am
interested in calculating impact of sex (F or M) on causing difference
between both groups e.g. I am interested in following 4 contrasts:
X1 (F) > X1 (M)
X2 (F) > X2 (M)
X1 (F) > X2 (F)
X1 (M) > X2 (M)
X1 (M+F) >
need to use a per-voxel
> regressor (--pvr option to mri_glmfit). Search through the archives to find
> examples where I've helped others
>
>
>
> On 2/6/18 12:36 PM, Martin Juneja wrote:
>
> Hi,
>
> I am interested in correlating cortical volume measures with behavioral
Hi,
I am interested in correlating cortical volume measures with behavioral
data X1, after regressing out the effect of age and sex. For that I ran
following commands:
mri_glmfit --y lh.X1.CV.15.mgh --fsgd X1.fsgd dods --C Corr-X1-cor.mtx
--surf fsaverage lh --cortex --glmdir lh.X1_CV.glmdir
with LGI?
>
> On Dec 22, 2017, at 4:33 PM, Martin Juneja <mj70...@gmail.com> wrote:
>
> Hi,
>
> I came across several papers e.g. http://www.sciencedirect.
> com/science/article/pii/S2213158215000856 where gyrification index (GI)
> is indicated in 'mm'.
>
> By
Hi,
I came across several papers e.g.
http://www.sciencedirect.com/science/article/pii/S2213158215000856 where
gyrification index (GI) is indicated in 'mm'.
By definition GI is the ratio of two quantities: inner contour/outer
contour (http://en.citizendium.org/wiki/Gyrification), therefore,
t;
> 6) PHC = parahippocampal complex
>
> 7) PFCmp = I think mp stands for medial posterior, but I am not super
> sure, you probably want to visualize this and double check.
>
> Thanks,
> Thomas
>
> On Thu, Oct 19, 2017 at 1:16 AM, Martin Juneja <mj70...@gmail.com> w
20130526, 2014
>
> Thanks,
> Thomas
>
> On Wed, Oct 18, 2017 at 3:48 AM, Martin Juneja <mj70...@gmail.com> wrote:
>
>> Hi experts,
>>
>> I am using Yeo atlas (7 networks) in my analysis. Where can I fi
Hi experts,
I am using Yeo atlas (7 networks) in my analysis. Where can I find name of
all the regions involved in each of these 7 networks in Yeo atlas?
Thanks.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Thank you so much Douglas. That's really helpful.
On Mon, Sep 18, 2017 at 2:41 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
>
> On 09/18/2017 05:35 PM, Martin Juneja wrote:
> > Dear Douglas,
> >
> > Thanks a lot for your reply.
> > Could y
then there is no need to add a number
to threshold? Whats the best approach to run this command?
I am really confused here and would really appreciate any clarification on
this.
Thanks a lot.
On Mon, Sep 18, 2017 at 2:20 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
>
> On 09/15/2017 0
Hi experts,
To calculate simulations on LGI measures, I ran:
mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd
--sim-sign abs --cwpvalthresh .05
But it gives error: ERROR: design matrix is not orthogonal, cannot be used
with permutation.
I came across a post where its
Hi experts,
I have a follow up question:
In case I wanted to add another covariate in contrast matrix e.g. in
addition to age and gender if I want to add BMI as another covariate in
calculating correlation between volume and LGI (as mentioned in previous
email), could you please confirm if
Hello FS experts,
I am correlating some of the behavioral measures with cortical thickness
(CT) and cortical gyrification (CG) measures.
- For CT-behavioral: I have some expected results after correcting for
multiple comparisons using mri_glmfit-sim
- For CG-behavioral: Again, I have some
Hi,
I need a general advice from the experts out there.
I am comparing cortical measures (thickness and volume) between controls
and patients using FreeSurfer. I used 'age' and 'gender' as covariates (in
fsgd file) while calculating group differences.
I was wondering even if I removed the
Hi,
One of my papers is under review showing significant differences in
cortical surface area between healthy controls and patients.
In this paper, regarding statistical results, for multiple comparison
correction, I ran Monte Carlo simulations using following command:
mri_glmfit-sim \
ne is MNI and one it Tal? can you send a summary of your
> commands?
>
> On 8/4/17 2:09 PM, Martin Juneja wrote:
>
> Hi FreeSurfer experts,
>
> I am trying to correlate my behavioral data with whole brain cortical
> measures using cortical measures as IVs and behavioral data DV.
>
Hi FreeSurfer experts,
I am trying to correlate my behavioral data with whole brain cortical
measures using cortical measures as IVs and behavioral data DV.
Somehow the significant clusters I get from cortical thickness, area and
volume are in MNI co-ordinates but significant clusters from local
you running FDR and cluster
> correction?
>
>
> On 05/11/2017 06:39 PM, Martin Juneja wrote:
> > In addition to that: I am always getting positive correlations (when I
> > load sig.mgh) every time i.e. even when I correlated thickness and
> > gyrification. None of
In addition to that: I am always getting positive correlations (when I load
sig.mgh) every time i.e. even when I correlated thickness and gyrification.
None of the voxels/areas showing negative correlation between any of the
structural measures
On Thu, May 11, 2017 at 11:26 AM, Martin Juneja
Hi Dr. Greve,
I am sorry for reposting this. Could you please confirm the following steps
and correct me where I am wrong.
Thanks.
-- Forwarded message --
From: Martin Juneja <mj70...@gmail.com>
Date: Tue, May 9, 2017 at 12:15 PM
Subject: Re: [Freesurfer] Maps s
normal, but when you create your contrast file, make sure to add
> a column to handle the per-vertex regressor. Eg, if you have two groups,
> then you would create a contrast [0 0 1] to test for the effect of the
> PVR. When you run mri_glmfit, just add --pvr lgi.mgz
>
>
>
> O
Hi everyone,
I have a question for stat experts.
I calculated cortical thickness for a region X for a group of patients
(Group A: At baseline and after treatment A). Then I calculated cortical
thickness for same region X for a group of patients (Group B: At baseline
and after treatment B).
I
wrote:
> You have to use the --pvr option to mri_glmfit. Run it with --help to
> get more info and write back if you still have questions
>
>
> On 04/26/2017 08:33 PM, Martin Juneja wrote:
> > Hello FreeSurfer experts,
> >
> > I came across a paper:
> > htt
Hello FreeSurfer experts,
I came across a paper:
http://www.sciencedirect.com/science/article/pii/S0166432815001837
where correlation maps between volume and gyrification are reported.
I am familiar with GLM in FreeSurfer i.e. correlating behavioral measures
with volume and gyrification but I
t sure what's
> input file here?
>
> Also, I am trying to correlate LGI versus behavioral score, regressing out
> the effect of sex and age. So I just wanted to confirm if my design.txt and
> contrast.txt files are correct here. Please find both following:
>
> Design file (Var
male 73 29
S004 Male 48 39
...so on..
Contrast file as following:
0 0 0.5 0.5 0 0 (same as *.mtx file used for glm_fit)
Thank you so much for your help and time.
On Tue, Mar 7, 2017 at 10:49 AM, Martin Juneja <mj70...@gmail.com> wrote:
> Hi Antonin,
>
> Thanks a lot fo
> Antonin
>
>
> If you don't have an orthogonal design, then you can't use
> mri_glmfit-sim. I think you can use PALM:
>
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
>
> I have not tried it yet.
>
> Anderson, can you use PALM with surfaces?
>
>
>
>
see mri_glmfit-sim --help).
>
>
>
> On 03/06/2017 01:36 PM, Martin Juneja wrote:
> > Hello everyone,
> >
> > I am trying to extract clusters showing significant correlation
> > between LGI and a behavioral measure. I am able to extract PCC and
> > sig.m
.
On Mon, Mar 6, 2017 at 2:00 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> I think you might be doing something wrong during preprocessing. Can you
> send your command lines?
>
>
> On 03/06/2017 12:11 PM, Martin Juneja wrote:
> > Hello experts,
> >
>
Hello everyone,
I am trying to extract clusters showing significant correlation between LGI
and a behavioral measure. I am able to extract PCC and sig.mgh but at the
last step when I try to run simulation command to view corrected results
and I run:
mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir
of a vertex" in mm3 (for surface area it is
> in mm2). Not sure what you mean about the actual volume values in the
> 20-40k range.
>
>
> On 02/14/2017 04:34 PM, Martin Juneja wrote:
> > Hi,
> >
> > I have a very simple question.
> >
> > I have
Hi Antonin and Thomas,
Thanks a lot for your reply.
I just wanted to confirm once again with you following steps.
I ran:
(1). mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi
lh --sval-annot lh.Yeo2011_7Networks_N1000.annot --tval
Hi,
I have a very simple question.
I have cortical volume maps (averaged over 30 subjects). I can view those
in FreeView using lh.pial overlaid with lh.mean.volume.mgh file. In overlay
> configure option, I had to set the min as 0 and max as 4 to display the
average volume. Now the color bar is
Hi everyone,
I was wondering if someone could please address the following question
regarding FreeSurfer usage.
I would really appreciate any help.
Thanks.
Hi,
I used following command to extract LGI values from a set of subjects:
recon-all -s -localGI
Output stats is saved in
Hi,
I used following command to extract LGI values from a set of subjects:
recon-all -s -localGI
Output stats is saved in lh.aparc_lgi.stats file. By default, its
calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am
interested in calculating LGI values using Yeo atlas of
Hi,
I used following command to extract LGI values from a set of subjects:
recon-all -s -localGI
Output stats is saved in lh.aparc_lgi.stats file. By default, its
calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am
interested in calculating LGI values using Yeo atlas of
Hi,
I am really sorry for re-sending this message. I would really appreciate
any response.
Thanks.
Hi FreeSurfer experts,
My goal is to extract cortical thickness of several ROIs, which are in
volume space. I am following instructions from this page:
-- Forwarded message --
From: Martin Juneja <mj70...@gmail.com>
Date: Tue, Jan 31, 2017 at 4:38 PM
Subject: Cortical thickness from ROI in volume format
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Hi FreeSurfer experts,
My goal is to extract cortic
-- Forwarded message --
From: Martin Juneja <mj70...@gmail.com>
Date: Tue, Jan 10, 2017 at 5:32 PM
Subject: Editing annot files
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Hi,
I was wondering if there is any way to edit annot file e.g. I would
Hi,
I was wondering if there is any way to edit annot file e.g. I would like to
edit *lh.Yeo2011_7Networks_N1000.annot* file in such a way when I overlay
this file in freeview, I just display limbic network from Yeo 7 network
atlas and hide other 6 networks.
I would prefer to use MATLAB for this
> You will need to create the yeo parcellation for each subject as well as
> run mris_anatomical_stats to create the stats file, then run
> aparcstats2table specifying the new stats file. Look in the
> recon-all.log file to see how to call mris_anatomical_stats
>
>
> On 12/14/2016 0
Hi,
I would like to use aparcstats2table command. By default, it uses
Killiany/Desikan
parcellation atlas. But I would like to use atlas by Yeo and colleagues (
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
Could you please let me know how can I use this atlas instead
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