Dear freesurfer experts,
I have some questions about the statistical model in freesurfer. In my
experiments, I would like to compare the cortical thickness of two groups
(schizophrenia patients and healthy controls) with age and sex as covariates.
I want to know that the variable in fsgd file
Dear list,
I have created flat maps of Freesurfer ROIs and manipulated them in Matlab to
extract only the area of the ROI that I am interested in. Now, I would like to
project the selected region onto the cortical mesh representation. Is there a
way to know the correspondence between points on
Hi Doug
Indeed, you had answered my post previously, but so promptly that I
missed it! My bad..
I have now re-run the analysis with the --jac option, and I do indeed
now obtain the same results with both methods.
Thanks a lot!
Julien
> Message: 17
> Date: Tue, 22 Sep 2015 10:03:56 -0400
> Fr
Thank you!
> Hi Angela
>
> you can load it into matlab with read_curv. If you have the surface and
> the
> tal xform (or transform the surface before loading it into matlab) you can
> find the point on the surface that is closest to a given tal coord and
> read
> out the sulc at that point
> cheer
Hi Jinsong
do you mean some of the values are not 1? By default I believe vol2vol uses
trilinear interpolation. Try including the option --nearest to use nearest
neighbor instead
cheers
Bruce
On Wed, 23 Sep 2015, Jinsong Tang wrote:
Hello,
I am try to convert some binary mask (0,1) to na
Hi Roberta
the surface indices are preserved in the flat maps and can be used to
lookup the coordinates on any of the surfaces.
cheers
Bruce
On Thu, 24 Sep 2015, Roberta
Santoro wrote:
> Dear list,
>
> I have created flat maps of Freesurfer ROIs and manipulated them in Matlab to
> extract onl
Hi Scott,
If you send me your subject, I can take a look.
https://gate.nmr.mgh.harvard.edu/filedrop2/
Best,
Lee
On Thu, 24 Sep 2015, Scott Quadrelli wrote:
Hi All,
I have a question re: the free surfer QA tool. I have run the script for
several subjects and notice that the talairach registr
Hello Bruce,
Yes, this works.
Thanks,
Jinsong
On Thu, Sep 24, 2015 at 5:35 AM, Bruce Fischl
wrote:
> Hi Jinsong
>
> do you mean some of the values are not 1? By default I believe vol2vol
> uses trilinear interpolation. Try including the option --nearest to use
> nearest neighbor instead
>
> c
Hello FSers,
quick question on the validity of FS automatic segmentation.
I have found longitudinal changes in hippocampus/amygdala volumes. Upon visual
inspection, there are some concerning issues, such as the labelling of CSF in
the amygdala. Mostly, these amount to a few clusters of between 5-
Thank you for the response Lee!
I was able to locate all the files now. To extract the perirhinal cortex
from rh.BA_exvivo.annot, would I just use mri_annotation2label command?
On Thu, Sep 17, 2015 at 3:43 PM, Lee Tirrell
wrote:
> Hi Priyanka,
>
> The cortical labels are exactly the same for
Dear Freesurfer experts,
I've been having issues with the trac-prep script opening the bvals file
within the dmri folder that it creates. Below is the full log of the
current error.
When I run:
ls -l /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals,
I get the below:
-rw-rw-r-- 1
Hi Karuna - Which build of freesurfer are you using? It's written in this
file: $FREESURFER_HOME/build-stamp.txt
a.y
On Thu, 24 Sep 2015, Karuna Subra wrote:
Dear Freesurfer experts,
I've been having issues with the trac-prep script opening the bvals file within
the dmri folder that it
c
Hi Karuna - Please read my question again. What's in the build stamp file?
a.y
On Thu, 24 Sep 2015, Karuna Subra wrote:
Hi Anastasia,
We're using version freesurfer 5.3.
On Thu, Sep 24, 2015 at 8:43 AM, Anastasia Yendiki
wrote:
Hi Karuna - Which build of freesurfer are you using? It
Hi Garret,
this is not really a longitudinal question, rather what accuracy can be
expected and when do you need to do aseg edits. I therefore changed the
title.
From what I know, a few voxels here and there will not change the
volume measures much. Furthermore, there should be some partial v
Hi Priyanka,
I believe there should already be a perirhinal label created (the
?h.BA_exvivo.annot is created by combining together a few labels).
Try seeing if these files exist with this command (replacing subject_name with
your subject):
ls $SUBJECTS_DIR/subject_name/label/*perirhinal*.lab
Hi Anastasia,
We're using version freesurfer 5.3.
On Thu, Sep 24, 2015 at 8:43 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Karuna - Which build of freesurfer are you using? It's written in this
> file: $FREESURFER_HOME/build-stamp.txt
>
> a.y
>
>
> On Thu, 24 Sep 2015, Ka
Feel free to upload a representative subject and we will take a look
Cheers
Bruce
> On Sep 24, 2015, at 11:54 AM, Martin Reuter
> wrote:
>
> Hi Garret,
> this is not really a longitudinal question, rather what accuracy can be
> expected and when do you need to do aseg edits. I therefore chan
Yes, below is what is in the build-stamp.txt:
freesurfer-Linux-centos4-stable-pub-v5.3.0
On Thu, Sep 24, 2015 at 8:47 AM, Karuna Subra wrote:
> Hi Anastasia,
>
> We're using version freesurfer 5.3.
>
> On Thu, Sep 24, 2015 at 8:43 AM, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
It sounds like a problem that was specific to the centos4 build, and that
should be solved in the latest tracula update. You can download the update
from here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
VERY IMPORTANT: Use the link that says "CentOS 4 (32-bit)", so that
Thank you, Anastasia. I'll try that now.
On Thu, Sep 24, 2015 at 9:14 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> It sounds like a problem that was specific to the centos4 build, and that
> should be solved in the latest tracula update. You can download the update
> from her
Hi again,
I do have the following files in the label directory:
lh.perirhinal_exvivo.label
lh.perirhinal_exvivo.thresh.label
rh.perirhinal_exvivo.label
rh.perirhinal_exvivo.thresh.label
I want to get the right perirhinal cortex in the .nii format for further
analysis. How can I get that?
Thanks
cd $SUBJECTS_DIR/$subject/mri
set hemi=lh
mri_label2vol --labe ${hemi}.perirhinal_exvivo.thresh.label \
--regheader \
../mri/norm.mgz \
--fill-ribbon \
--subject $subject \
--hemi $hemi \
--o ${hemi}.peri.nii.gz
should do the trick
cheers
Bruce
On
Hi Bruce,
as you can see in attached image, the hippocampal label (brownish) seems to
bleed into 3-4 rows of voxels into a ventrical. In the "amg" image, the
amygdala volume (light blue) seems to "wrap" on the outside around the
hippocampus a bit, when obviously it should be more spherical. Thes
Hi Garret,
again, I am not an editing expert, but some of these look more severe.
The question is what you need this for. If this is a population study
with 1000 of subjects then obviously editing will be tough. For a small
study I would recommend manual edits to make sure you are removing as
Hello,
When I use aparcstats2table to pull thickness values of the Desikan atlas, I
get a value of zero for two of my subject’s insula thickness in both
hemispheres. For these two subjects, I also get values for
“lh_unknown_thickness” and “lh_corpuscallosum_thickness”, while all of the
other s
Hi Martin,
the sample is small (30), and the design is longitudinal, but these structures
are not the main focus, which is CT (already manually edited).
Thanks for help,
Garret
Date: Thu, 24 Sep 2015 14:14:52 -0400
From: mreu...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject:
Dear Freesurfers,
I wanted to ask you if you know how can I convert a .mgh file to a .obj
file.
I want to run surfstats (specifically SurfStatReadSurf ) but it does not
read .mgh files (i.e, the surface file; lh.w-g.pct.mgh.fsaverage.mgh).
Although, it reads the lh.white, but I need the average,
when you say "it does not work either', what do you mean? Please remember
to send us the entire screen output of commands you are asking about
On Thu,
24 Sep 2015, Myriam Oliver wrote:
> Dear Freesurfers,
>
> I wanted to ask you if you know how can I convert a .mgh file to a .obj
> file.
>
> I
Hello FreeSurfer Experts,
This question has been asked before by someone and I am looking to do
something similar.
*If this isn't possible, could we obtain this from fsaverage? I noticed **that
$FREESURFER_HOME/subjects/fsaverage does have an aparc+aseg.mgz *
*is there also a way to get wmparc.
Hi Martin,
I wanted to ask about getting the stacked SPC values for use with
mri_glmfit. I ran the following long_mri_slopes command but cannot
identify which if any is the stacked spc mgh file:
long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness
--hemi lh --do-avg --do-rate
Hi Martin,
Sorry i have just realised that I need to add the --stack-spc flag to my
long_mris_slopes command to get the stacked file for my glm analysis. I
now have three other questions about long_mris_slopes:
1. When you run --isec-lables with the flag --meas thickness, is the
output file sp
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