Hello FreeSurfer experts,
I am working on resting-state functional connectivity using freesurfer by
following the instructions from:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
I made sure that the seed region (for ever subject) I am using is at the
correct pl
wrote:
> what was your mkanalysis-sess command?
>
> On 06/08/2016 02:10 PM, Martin Juneja wrote:
> > Dear FreeSurfer and SPM experts,
> >
> > I am trying to calculate functional connectivity maps using FreeSurfer
> > pipeline:
> >
>
Hello FS experts,
I have a data set of 20 subjects (patients) collected at location-1 with 3T
Siemens scanner. Also, I have a set of age-matched 20 subjects (controls)
collected at location-2 with 3T Siemens scanner.
I am interested in comparing cortical thickness between controls and
patients us
, 2016 at 12:02 PM, Douglas N Greve wrote:
> You can do the comparison, but the interpretation is difficult. If you
> see a difference, how do you know it is not due to the scanner? There's
> not much you can do ...
>
>
> On 09/29/2016 02:54 PM, Martin Juneja wrote:
> >
0.0138 -0.032545.4015
-0. -0. -0. 1.
Thanks a lot.
On Mon, Oct 3, 2016 at 11:42 AM, Douglas N Greve
wrote:
> I would still say no -- the differences could still be due to
> differences in acquisition parameters
>
>
> On 10/03/2016 02:30 PM
lematic. You
> will get more smoothing with the 1.3mm (ie, partial volume effects), and
> that could easily show up in the thickness measurements
>
>
> On 10/05/2016 12:19 PM, Martin Juneja wrote:
> > Hi Dr. Greve,
> >
> > After I compare the two protocols (a
Hi everyone,
I am trying to use following command to save stats from a set of subjects
in a table format:
aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt
But after I run this, I get following error:
Traceback (most recent call last):
File "/usr/local/freesurfer/bin/apa
pecting the qdec table to actually variables in it. Can you try adding
> variables? Also, try it without the --qdec flag instead specifying the
> subjects with --subjects HC003_1 HC004_1 ...
>
> On 11/8/16 8:09 PM, Martin Juneja wrote:
>
> Hi everyone,
>
> I am trying to use fo
and (c) how can I display it on
standard fsaverage for publications purpose?
On Wed, Nov 9, 2016 at 10:52 AM, Douglas N Greve
wrote:
> can you send the qdec file with variables?
>
>
> On 11/09/2016 11:51 AM, Martin Juneja wrote:
> > Hi Dr. Greve,
> >
> > Somehow eve
Hi,
I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine
whether the DTI data (in DICOM format) I have is multi-band sequence?
I used dicominfo in MATLAB but couldn't find any information related to
multi-band in the dicom header.
Any help would be really appreciated.
__
le to just pull that
> field on one volume and compare the field for all slices and see if
> any of them have the same time.
>
> hth
> d
>
> On Wed, Nov 30, 2016 at 12:10 PM, Martin Juneja wrote:
> > Hi,
> >
> > I was wondering if there is any way in FreeSur
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
o 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 03:56 PM, Martin Juneja wr
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
-- Forwarded message --
From: Martin Juneja
Date: Tue, Jan 10, 2017 at 5:32 PM
Subject: Editing annot files
To: Freesurfer support list
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
Hello everyone,
I am very new to FreeSurfer. Although I know what smoothing means etc. but
I am not sure what smoothing level is the best to choose while comparing
cortical thinning for patients vs. controls. Qdec gives several options to
choose from among 0, 5, 10, 15, 20 and 25.
Literature says
Hello everyone,
I am following this page to process fMRI data:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
I am able to run until step-3 but at step 4, I am not sure what should be
directory to run this command. If I run the command in SUBJECTS_DIR
directory,
(after
overlaying over inflated surface), it doesn't display anything and gives me
error "freadFloat: fread failed".
I would really appreciate any suggestions how can I display functional
connectivity maps?
Thanks,
MJ
On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja wrote:
> Hel
>
>$> tksurferfv fsaverage lh inflated -ov sig.nii.gz -fminmax 2 3
>
> -Zeke
>
>
> On 04/26/2016 04:07 PM, Martin Juneja wrote:
> > Hello again,
> >
> > Somehow I figured out the error I had related to *.config. Now I am able
> > to run successful
Dear FreeSurfer experts,
I am using FsFast functional connectivity walkthrough steps to analyze fMRI
data from:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
I am able to run all these steps successfully and can view the voxel-wise
distribution maps.
I was wond
Hi all,
I am trying to perform step-3 from the instructions here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
But I do not have segid because the LookUp table FreeSurfer creates after
running recon-all doesn't have the area I am interested in. So I defined
the
Dear FS experts,
I just finished calculating functional connectivity maps using FreeSurfer.
I just want to confirm if the following steps I used are correct:
(1). I defined configured seed regions parameters using fcseed-config
command, say R01.config and R02.config and created seeds using fcseed
#x27;ll want to use pcc or ces. Otherwise looks ok.
> doug
>
> On 05/06/2016 12:03 PM, Martin Juneja wrote:
> > Dear FS experts,
> >
> > I just finished calculating functional connectivity maps using
> > FreeSurfer. I just want to confirm if the following steps I use
Greve
wrote:
> Yes, those are the right commands. That will give you the ces (the
> regression coefficient). Typically, people use the pearson correlation
> coefficient (pcc), but I have not seen many differences between the two.
>
> On 05/06/2016 05:13 PM, Martin Juneja wrote:
> &
I would suggest you to check if preproc is done using the argument
-mni-305-2mm.
On Wed, May 11, 2016 at 12:48 PM, Sahil Bajaj wrote:
> Hi Dr. Greve,
>
> This works for me if I define seeds into subject-wise anatomical space.
>
> Now, location of seed regions across subjects might differ because
-- Forwarded message --
From: Martin Juneja
Date: Tue, Jan 31, 2017 at 4:38 PM
Subject: Cortical thickness from ROI in volume format
To: Freesurfer support list
Hi FreeSurfer experts,
My goal is to extract cortical thickness of several ROIs, which are in
volume space. I am
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:
https://surfer.nmr.mgh.harvard.edu/fswiki/V
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 7
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 7
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 lh.aparc_lgi.
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 s
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
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_7Netwo
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 cortical volume maps (averaged o
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 --cac
.
On Mon, Mar 6, 2017 at 2:00 PM, Douglas N Greve
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,
> >
> > I am trying to correlate c
>
>
> 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.mgh but at the last step when I try to ru
te.avg.area.mgh) file.
>
> 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 P
03 Female 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 wrote:
> Hi Antonin,
>
> Thanks a lot for your reply.
>
27;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 (Variables
; file
>> > > with design matrix, then rename it to Xg.csv to be correctly readable by
>> > > PALM.
>> > >
>> > > Regards,
>> > >
>> > > Antonin
>> > >
>> > >
>> > >
>> >
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 was
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:
> > http://www.sciencedirect.co
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 hav
r 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
>
>
>
> On 04/27/2017 06:13 PM, Martin Junej
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
Date: Tue, May 9, 2017 at 12:15 PM
Subject: Re: [Freesurfer] Maps showing correlations between
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
r
> 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 the voxels/areas showing
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
d 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.
>
> Somehow the signifi
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 \
--cach
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 effect
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 expect
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 followi
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 mentioned
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
wrote:
>
>
> On 09/15/2017 02:13 PM, Martin Juneja wrote:
>
Thank you so much Douglas. That's really helpful.
On Mon, Sep 18, 2017 at 2:41 PM, Douglas N Greve
wrote:
>
>
> On 09/18/2017 05:35 PM, Martin Juneja wrote:
> > Dear Douglas,
> >
> > Thanks a lot for your reply.
> > Could you please clarify why
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
https://mail.nmr.mgh.harvard.edu
hanks,
> Thomas
>
> On Wed, Oct 18, 2017 at 3:48 AM, Martin Juneja wrote:
>
>> 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?
>>
>> Tha
pal 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 wrote:
>
>> Dear Dr. Yeo,
>>
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, shoul
t;
> On Dec 22, 2017, at 4:33 PM, Martin Juneja 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 definition GI is t
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
mri
or (--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
> data X1, after regressi
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) > X2
at 3:18 PM, Martin Juneja 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 contrasts:
>
> X1 (F) &
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
whethe
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
wrote:
>
>
> On 02/24/2018 12:00 AM, Martin Juneja wrote:
> > Hi experts,
> >
> > I am not sure if this has a
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 pa
>
>
> 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
(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
>
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
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 dif
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 s
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.
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
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 <
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
(s
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 fa
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 outp
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
To
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
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
c
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
t; I'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 differ
rvature 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
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:
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 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 to
t 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: *[Freesurf
rparing was done prior 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
> >&
t and 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 detail
; 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
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 Ag
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
: 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,
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 m
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
SPSX/lh.SPS_vol.glmdir/mask.m
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 w
040 3526-6733.96 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 t
:
> sorry, 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, Marti
1 - 100 of 122 matches
Mail list logo
