Hi Ani
the jacobian of white? The Jacobian we write out is the Jacobian of the
spherical registration, which is independent of the pial surface
cheers
Bruce
On Tue, 20 Jun 2017, Aniqa DaAsliLovr wrote:
Hi All,
I have two questions.
1) Is there a way to calculate a pial surface jacobian ?
can you include your full command line? It looks like you typed:
recon-all -autorecon2-wm -autorecon3 -Subj2
when probably what you wanted was
recon-all -autorecon2-wm -autorecon3 -s Subj2
cheers
Bruce
On Tue, 20
Jun 2017, Michael Davies wrote:
Hello, i am currently having problems with
Hi Bruce, i tried your suggestion but it is saying Missing file name. Do i need
to include wm.mgz in the command line?
Regards, Michael
bash-4.1$ freesurfer_setup_freeview
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Setting up environment for FreeSurfer/FS-FAST (
Dear Doug,
thanks again.
Will look into which is the best for LGI (if any).
Best wishes
Marco
On Tue, Jun 20, 2017 at 7:48 PM, Douglas Greve
wrote:
>
>
> On 6/20/17 2:42 PM, marco mcsweeney wrote:
>
> Dear Doug,
>
> thanks again. I used mri_info --sres orig.mgz (T1.mgz) and got output 1.
> I
Hello, i am currently having problems with the code required to regenerate the
surface when editing the WM Volume. I was wondering if you could provide any
tips or advice as to where i am going wrong please?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
freesurfer-Linux-cen
On 6/20/17 2:42 PM, marco mcsweeney wrote:
Dear Doug,
thanks again. I used mri_info --sres orig.mgz (T1.mgz) and got output 1.
I assume this is 1mm thickness?
yes
Also, in terms of using eTIV or total gray matter volume, which do you
think would be the best to use as nuisance factor when l
Dear Doug,
thanks again. I used mri_info --sres orig.mgz (T1.mgz) and got output 1.
I assume this is 1mm thickness?
Also, in terms of using eTIV or total gray matter volume, which do you
think would be the best to use as nuisance factor when looking at cortical
thickness as well as LGI?
Thanks a
Hi All,
I have two questions.
1) Is there a way to calculate a pial surface jacobian ? How do I get this
measure ?
2) Is the lh.jacobian_white rh.jacobian_white the deformation to fsaverage
or something else ?
Please let me know.
Thanks
Ani
___
Free
mri_info --sres file.mgz will give you the slice thickness
you should at least control for the slice thickness by creating a new
binary factor, so if you had 2 groups, you'd have 4 groups (this is the
design matrix not the contrast matrix)
On 6/20/17 11:58 AM, marco mcsweeney wrote:
Dear Do
Yes the matlab runs well. I remember that I have met some error like “ERROR:
cannot find matlab. Is it in your path?” Then I recognize that I always open
matlab by typing capital MATLAB rather than lowercase. So I copied
/usr/local/MATLAB/R2016b/bin/glnxa64/MATLAB as
/usr/local/MATLAB/R2016b/b
Hi Daniele,
as others commented, the stream is unbiased so the order does not affect
results, so you are fine. That said, if you switch the order around you will
get slightly different results due to numerical reasons (small differences
affected by the order that accumulate to produce noticeab
"vintage" is one way of putting a positive spin on it I guess :)
Unfortunately I dont have any leads on how to resolve the issue, and we
dont have adequate resources to devote to these tools.
On 06/20/2017 10:42 AM, Caspar M. Schwiedrzik wrote:
> Hi!
> We are running Freesurfer on a central se
Dear Doug,
I have a few final questions, my apologies.
The study I am working on is a retrospective study, which is not ideal. As
a result, although all of the individuals in the study were scanned on the
same 3T scanner, all of the healthy controls have 1.6mm slice thickness and
most of the pati
The low pass filter is not required, just set the lpf cutoff freq to 0.
For detrending, set the nuisance regressors with the -xreg flag. The
polynomial detrending order is set by the highpass cutoff freqency. You
can play with it to get a 5th order polynomial. There is no equivalent
to the -h
this appears to be some kind of matlab problem. Can you otherwise run
matlab ok?
On 6/15/17 5:17 PM, 杨国春 wrote:
Hello FreeSurfer Developers,
I'm attempting to run 1st-level analysis with FS-FAST, following the tutorial
here
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastF
rawavg.mgz should have exactly the same dimensions as 001.mgz. orig.mgz
and downstream volumes will be cropped. Is that what you mean? To get
back to the native space, look at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 6/15/17 4:23 PM, Jerry Jeyachandra wrote:
Hi Free
or don't run so many at the same time
cheers
Bruce
On Tue, 20 Jun 2017, Douglas Greve
wrote:
>
> The error was earlier:
>
> CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory.
> Abort (core dumped)
> ERROR: mri_ca_register with non-zero status 134
>
> looks like you need
Well, neither thickness nor surface area are gaussian to begin with, so
volume is definitely non-gaussian. I'm not sure how much difference that
will make in terms of parametric statistics. You can do permutation
using mri_glmfit-sim if you have an orthogonal design. If not, you can
use PALM b
no, the longitudinal anlaysis is be design insensitive (and unbiased!)
w.r.t. the order of the timepoints
cheers
Bruce
On Tue, 20 Jun 2017, Daniele Orlandi
wrote:
Dear experts,
any suggestion about my question? (see below)
Thank you in advance!
Daniele
\- Messaggio originale -
\Da
Dear Doug,
OK thank you so much for all of your help.
Best wishes
Marco
On Tue, Jun 20, 2017 at 3:58 PM, Douglas Greve
wrote:
>
>
> On 6/20/17 10:43 AM, marco mcsweeney wrote:
>
> Dear Doug,
>
> thank you.
>
> I will go ahead with DOSS through the command line. I did find significant
> diff
Thanks Dr Douglas for your reply. Following is the list of command I used
to generate brainstem mask.
- I first created from average subject directory, mask of brainstem
using mri_binarize command:
mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz
- Then converted to mni305 spac
On 6/20/17 10:43 AM, marco mcsweeney wrote:
Dear Doug,
thank you.
I will go ahead with DOSS through the command line. I did find
significant differences (FDR corrected) with DOSS in QDEC.
Hopefully they will still be present through the command line. It will
be interesting to see if I get t
Dear Doug,
thank you.
I will go ahead with DOSS through the command line. I did find significant
differences (FDR corrected) with DOSS in QDEC.
Hopefully they will still be present through the command line. It will be
interesting to see if I get the same results.
Sorry but just one more quick qu
Hi!
We are running Freesurfer on a central server and I don't have a second one
at hand with Freesurfer installed to test this, unfortunately.
It seems that Freeview is working fine now, so this may well have been just
a hickup.
However, the problem persists with tkmedit. If you had any leads on ho
I don't think those are actually labeled. Use the White-Matter and
Cortex labels for cerebellum.
On 6/19/17 11:09 AM, M Janani wrote:
Hi freesurfer team,
I apologize, I am new to freesurfer.
I’m doing analysis on PiB. I have successfully got my
.stats files
On 6/20/17 10:14 AM, marco mcsweeney wrote:
Dear Doug,
thank you so much for getting back to me on this.
I am using Freesurfer version 5.3 with QDEV version 1.4 which gives me
both DODS and DOSS design matrix options. I am a little confused about
DOSS in QDEC as I have read quite a few publ
Thanks Jose. You might also be interested in the PETSurfer
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer. It has everything
you need to do PET analysis in the volume or the surface using PVC or
not. It currently has MRTM and MRTM2 kinetic modeling, but you might be
able to interface your
Sorry, qdec has been slowly losing functionality because no one here is
maintaining it. This feature looks like one of the casualties.
On 6/19/17 9:27 AM, Hossein Rejali wrote:
Hello,
I'm fairly new to freesurfer, I've been going through the tutorials to
get my hands dirty. Currently on the
Can you use annotval2surfoverlay.m ? it can be found in
$FREESURFER_HOME/matlab or here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
On 6/19/17 5:38 PM, Ismail Koubiyr wrote:
Dear all,
Would anyone have any idea how to display these p-values for each lobe
on a sur
how was it created?
On 6/20/17 9:41 AM, Dr Sampada Sinha wrote:
Dear freesurfer experts,
I am trying to over brainstem mask of my patients' group on
mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or
amygdala mask, but somehow the midbrain mask is shifted from the
actual p
The tktools like tkmedit and tksurfer are more-or-less deprecated and we
do sometimes get user reports about not accepting keyboard input.
However, freeview should work fine as we use Centos 7 platform for our
testing and have not seen any such issues for that application. Is it
possible for yo
Dear Doug,
thank you so much for getting back to me on this.
I am using Freesurfer version 5.3 with QDEV version 1.4 which gives me both
DODS and DOSS design matrix options. I am a little confused about DOSS in
QDEC as I have read quite a few publications which have used DOSS in QDEC
before. Can
Hi Daniele - A main feature of the freesurfer longitudinal stream is that it is
unbiased, i.e., it treats all the time points in the same way, regardless of
their order in time.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.m
The error was earlier:
CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory.
Abort (core dumped)
ERROR: mri_ca_register with non-zero status 134
looks like you need more memory in your gpu
On 6/20/17 7:30 AM, Ramesh Babu wrote:
Dear Expert,
The recon-all -all process has
DOSS should not be used with QDEC as it may or may not do the right
thing. Is it not disabled? What version are you using?
To answer your question, if you want to use DOSS and you're interested
in the diff bet groups, then first test for an interaction between group
and covariate. If that is n
Dear Expert,
The recon-all -all process has stopped abruptly and error report shows that
"cannot find or read transforms/talairach.m3z". Please see the attached
file. Processing was running in 5 terminal simultaneously and it has
happened for two processing. Others exited without error. Could plea
Dear experts,
any suggestion about my question? (see below)
Thank you in advance!
Daniele
\- Messaggio originale -
\Da: "Daniele Orlandi"
\A: freesurfer@nmr.mgh.harvard.edu
\Inviato: Venerdì, 16 giugno 2017 18:01:59
\Oggetto: Freesurfer Template Creation
\
\Dear experts,
\
\I'm runnin
Hey,
do you have any idea on what might be causing this error and how to install
this library?
Thanks!
Lisa
On 15 June 2017 at 16:20, Lisa Kramarenko wrote:
> Hi,
>
> sure, it's
>
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
>
> thanks!
>
> On 13 June 2017 at 19:38, Z K wrote:
>
>>
Dear Freesurfer experts,
I have a quick question regarding the appropriate design (DOSS or DODS) to
be used with QDEC when comparing 2 groups for cortical thickness and LGI
values.
So far I have used DODS first to look for an age-cortical thickness
interaction in both groups. I used the real ages
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