Dear FreeSurfer,
I would like to do the long. two stage model
(https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel)
Study design: 2 groups (one control group, one patient group) with gender and
age as covariates. Each subject was MRI scanned at baseline and 6 weeks
follow-up. I
I have found the reason for the error: FSGDF Format Error: file =
/Volumes/External/P1_FU/GroupDiffLhThickness.fsgd, tag=Input
The class should be 1.0 and 0.0, as stated in the fsgd file.
Otherwise, is the process still correct?
BW
Kasper
> Original Message
> Subject: problem
Hi Bruce,
I mean for the longitudinal analysis.
Forgot to mention this, sorry!
Kind regards,
Rose
Date: Fri, 11 Aug 2017 12:39:58 -0400 (EDT)
From: Bruce Fischl
Subject: Re: [Freesurfer] Test-retest reliability small subcortical
regions
To: Freesurfer support list
Message-ID:
Dear FreeSurfer Experts,
I was trying to compile the FreeSurfer code by following steps shown in
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page
However, I got this error message after I ran ./configure
configure: error: FATAL: netcdf lib not found. Set LDFLAGS or
--wit
please send error and all terminal output
On 08/14/2017 12:47 AM, Yi, Hyon-Ah wrote:
> Dear FS experts,
>
>
> I met an error when I try to run mris_preproc. Actually i succeeded
> this command with my own scripts and fsgd files before.
> There are 2groups with one covariates but I keep getting t
The mri_gtmpvc command will remove volume fraction effects. Look at the
PETsurfer page. Run it with --psf 0 and use the muller-gartner output.
The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
> Hi Shane
>
> we do have some tools to deal with it like
> m
Hi
I'm beginner of freesurfer and have an error while using recon-all. I'm Mac
(Sierra) user.
My subject's data is under:
/Applications/freesurfer/subjects/yeseul_data
After open terminal, I put commands like:
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFre
Hi Dr Greve,
Thank you very much! I will use the MGX CTX volume for the surface sampling.
Best Wishes,Shane.
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve
wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the
PETsurfer page. Run it with --psf 0 and use
what is your configure line? You may need to add something to point to
the mni library
--with-mni-dir="/usr/pubsw/packages/mni/1.5"
On 08/14/2017 10:32 AM, Aziz Nanthaamornphong wrote:
> Dear FreeSurfer Experts,
>
> I was trying to compile the FreeSurfer code by following steps shown
> in
> ht
first, run it with -subject sbj1_rec (ie, don't give it the full path).
There is something wrong with the dash before the "i". It looks like a
dash, but it is really something else. Did you cut and paste it from
somewhere? At the command line, Try deleting it and typing a dash.
On 08/14/2017 1
there is not an easy way to do it. Probably the easiest thing to do is
to create a separate session for each run. You can them analyze them
under the same analysis name, then combine them together with
isxconcat-sess, then do a one-sample group mean (--osgm) fixed effects
analysis in mri_glmfit
mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz).
can you elaborate on what you are trying to do? what do you mean by a
template?
On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to use the following command to merge the volume
you can use mri_aparc2aseg. Look in the recon-all.log file of an
individual for the command used to generate the wmparc.mgz.
On 08/01/2017 04:43 PM, Eryilmaz, H. Hamdi wrote:
> Hi Anastasia and FS experts,
>
> I am trying to create a white matter ROI mask underneath a cortical
> ROI label (e.g
If you use mri_gtmpvc, then the gtm.stats file will have the intensity
values.
On 08/11/2017 02:37 AM, M Janani wrote:
> Thanks for your support Douglas.
>
> I have processed my PIB PET images using PETSURFER. It works fine.
>
> I have one more query. Could you please help in computing the PiB m
I tried using it both as an input and output and the produced files both seemed
wrong, so I was trying different combinations.
The template (a picture of it is attached in my initial email) is a mask for
primary visual areas, and to export and use it in a different software I am
trying to super
[image: image.png]
--
*Emma Jane Rose PhD.*
*Assistant Research Professor & *
*Associate Director for the **Program for Translational Research on
Adversity and Neurodevelopment (P-TRAN)*
*Edna Bennett Pierce Prevention Research Center*
*The Pennsylvania State University*
*308 Biobehavioral Health
The Program for Translational Research on Adversity and Neurodevelopment
(P-TRAN) at The Pennsylvania State University is seeking a qualified
postdoctoral researcher with expertise in human brain imaging, specifically
magnetic resonance imaging (MRI)) with children and adolescents. This
position
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta
--psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01
--mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
You will need to run gtmseg --s subject (takes an hour or so), then add
--seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
> Hi Dr Greve,
>
> Are the settings correct to do partial volume correction of my MD images?
>
> mri_gtmpvc --i subject/dtrecon/adc.nii.gz --re
do the commands on this link get you where you need to be?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 08/14/2017 03:04 PM, Yagmur Ozdemir 19 wrote:
> I tried using it both as an input and output and the produced files both
> seemed wrong, so I was trying different combina
Dear experts,
I would like to download the most recent build of FreeSurfer development
version (linux 64 bit).
The origin/dev git repository contains commit up to today (14.8.17), but last
change of "daily build" of dev version is 28.7.17.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer
Dear experts,
I would like to ask, whether I could obtain a basic general info on samseg
routines - what specifically are they doing (publication reference) and how to
use them?
Regards,
Antonin Skoch
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Freesurfer@nmr.mgh.
It works now!
Thank you :)
On 15 August 2017 at 03:30, Douglas N Greve
wrote:
> first, run it with -subject sbj1_rec (ie, don't give it the full path).
> There is something wrong with the dash before the "i". It looks like a
> dash, but it is really something else. Did you cut and paste it fro
Dear FreeSurfer
I have read through a similar question/answer (again):
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53238.html
However, i still done seem to understand how to exactly pass the output of
long_stats_slopes into the following command with a C and fsgd file??
mri_g
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