Dear Experts,
I save the longitudinal sample data to the path:
/usr/local/src/freesurfer/subjects/long-tutorial, then run
d4201z-CELSIUS-M470-2:/usr/local/src/freesurfer/subjects/long-tutorial>
freeview -v OAS2_0001/mri/norm.mgz \? -f
OAS2_0001/surf/lh.pial:edgecolor=red \?
Dear experts,
About the differences between FSL and Freesurfer, I've noticed that the
left-hippocampus volumes measured by Freesurfer are always bigger than the
left-hippocampus volumes measured by FSL. Is there any reason that can
explain that?
According to the literature, the percent volume dif
Hi Ana
it can depend on your manual tracing protocol. For example: are
fimbria/alveus part of your definition of hippocampus? For us they are.
cheers
Bruce
On Tue, 2 Oct 2012, Ana Arruda wrote:
>
> Dear experts,
>
> About the differences between FSL and Freesurfer, I've noticed that the
> l
Hi Octavian
I'm not clear what you are asking. If recon-all completed, then the pial
surface is already registered to fsaverage via the ?h.sphere.reg surface
and you should be able to use mri_surf2surf to transfer the label into a
common space.
Bruce
On Mon, 1 Oct 2012, octavian lie wrote:
Dear FreeSurfer experts,
I'm processing scans on three different computers and I would like to know
if it is possible to collect all the processed scans together in order to
analyze data on just one computer.
I realized that even moving the processed subjects folders to another
folder within the
The manual protocol was made by doctors.They traced the hippocampus
segmentation based on their knowledge of anatomical structures.
For automatic segmentation I've used the following command:
recon-all -i input_suject_name -autorecon1 -autorecon2 -s
output_subject_name
and after this simulation
if their definition of what is and is not hippocampus differs from the
one we use then you will get different volumes. You need to find out what
they defined as part of it and see if it matches our protocol
cheers
Bruce
On Tue, 2 Oct 2012, Ana
Arruda wrote:
> The manual protocol was made by
Hi Pietro
you should be able to. When you say you can't run tksurfer/tkmedit what
happens? Can you send us screen output?
Bruce
On Tue, 2 Oct 2012, pietro de rossi
wrote:
Dear FreeSurfer experts,
I'm processing scans on three different computers and I would like to know
if it is possible t
Hi Yawu, look in the paper by Christophe Destriuex (2010 Neuroimage). It
gives a table of all these ROIs
doug
On 10/02/2012 02:29 AM, yawu Liu wrote:
> Dear Experts,
> How to know the full name of structures in the output? such as
> G_Ins_lg_and_S_cent_ins, S_oc-temp_med_and_Lingual...
> Rega
Hi Knut, when did you download mri_segstats? Can you send me the result of
mri_segstats --all-info
doug
On 10/02/2012 01:42 AM, Knut J Bjuland wrote:
> I have download the latest verion of mri_segstats from the release
> notes. But it does not generate asegstats.
>
>
> 4 x86_64 x86_64 GNU/Linux
>
Dear Experts,
What is the best way to get the average thickness for each subject in QDEC,
more exactly for the uncorrected clusters?
I know when running QDEC theer is a stats_tables file saved so I wonder if the
lh. aparc.thickness.stas.dat represents the mean cortical thickness.
Should this va
Hi Liz,
I have no idea about the progress of FS on 64 bit OSX. I think it should be
possible to run Linux in a virtual box. Both these questions can probably be
answered by Nick.
But I would recommend to first try to use a new version of mri_robust_template
from our dev version (if it goes thr
Hi Yawu,
can you just start freeview w/o any parameters. I think something is not setup
correctly on your system. Maybe someone else knows how to setup freeview on
ubuntu?
Best, Martin
- Original Message -
From: yawu Liu
To: freesufer
Sent: Tuesday, October 02, 2012 5:16 AM
Ok, this is what happened after I moved the folders to a storage device
(MacintoshHD2)
[HG-01881507-DM7:~] aitkenww% setenv SUBJECTS_DIR
/users/aitkenww/desktop/MacIntoshHD2/PROC_WILL
[HG-01881507-DM7:~] aitkenww% cd $SUBJECTS_DIR
/users/aitkenww/desktop/MacIntoshHD2/PROC_WILL: No such file or dir
That fact can explain the differences between manual and automatic
segmentations.
But how can I explain the differences just for the left-hippocampus values
in Freesurfer? Comparing percent volume difference between
Freesurfer-Manual and FSL-Manual, the percent is bigger in left-hippocampus
for Fre
I've just figured that out.the storage device icon is on the desktop
but the actual path to the storage device is differentvery silly
:-)
sorry for bothering
2012/10/2 pietro de rossi
> Ok, this is what happened after I moved the folders to a storage device
> (MacintoshHD2)
>
> [HG
Hello,
I have a set of archival data (so I was unfortunately not able to specify the
acquisition sequences and include the recommended MPRAGE sequence). I am
asking which sequence (if any) would be most conducive to volumetric/regional
analysis using FreeSurfer. A Philips Achieva 3.0T was use
Thanks Doug!
However, now I'm getting the following error:
*Resampling
Output registration matrix is identity
mri_vol2vol done
ERROR: canot find norm*
I am running:
*xhemireg --s fsaverage --reg*
Any suggestions? Should I run the following from
$SUBJECTS_DIR/fsaverage/mri/?
mri_nu_correct.mn
no worries. Glad it worked out
Bruce
On Tue, 2 Oct 2012, pietro de rossi wrote:
I've just figured that out.the storage device icon is on the desktop but
the actual path to the storage device is differentvery silly
:-)
sorry for bothering
2012/10/2 pietro de rossi
Ok, this is
maybe the fimbria/alveus is different on the left than the right? Not
sure, but if the protocols are different it's very difficult to make any
meaningful comparison
Bruce
On Tue, 2 Oct 2012, Ana Arruda wrote:
That fact can explain the differences between manual and automatic
segmentations. Bu
so no T1-weighted scans at all? If not, we probably won't be able to help
you
sorry
Bruce
On Tue, 2 Oct 2012, Sullivan, Patrick M. wrote:
Hello,
I have a set of archival data (so I was unfortunately not able to specify
the acquisition sequences and include the recommended MPRAGE sequence)
Hello experts,
I am getting skull strip issues with FreeSurfer recon-all runs in every data.
I ran recon-all on my T1-data and noticed that the skullstrip is not so good.
Almost in every subjects there were dura included, so I tried the suggestion
of using the flags -skullstrip and -Clean–bm an
Hi Deirdre
I'm not sure exactly what you mean, but probably what you are seeing (the
circular patterns) are the effects of motion
cheers
Bruce
On Tue, 2 Oct 2012, Deirdre
O Shea wrote:
> Hey everyone,
>
> I was wondering if anyone knew how to correct for a ripple like effect in
> the image. I
Hi Rashmi
getting rid of all the dura without removing any problem is exceedingly
difficult (if not impossible). Usually we live with some remaining dura
as it doesn't affect the surface placement much.
cheers
Bruce
On Tue, 2 Oct 2012, Rashmi
Singh wrote:
Hello experts,
I am getting skul
Thank you Bruce,
I certainly understand your point. In my study I am trying to use whole
brain volume to normalize my volumetrics data. Due to the inclusion of the
dura into brain, I may get variation in the whole brain volume across
subjects.
In addition the current issue is affecting the grayma
when did you update the xhemi scripts last? Do a search on our wiki for
xhemi to get pointers to the most recent ones
On 10/02/2012 01:59 PM, Andrew Bock wrote:
> Thanks Doug!
>
> However, now I'm getting the following error:
>
> /Resampling
> Output registration matrix is identity
>
> mri_vol2vo
Hi
I downloaded about Tuesday and this morning. However when I download a
bit later to day I got a working mri_segstats.It print out mri_segstats
--all-infoProgramName: mri_segstats ProgramArguments: --all-info
ProgramVersion: $Name: $ TimeStamp: 2012/10/02-19:57:40-GMT
BuildTimeStamp: Jun
I updated all the xhemi scripts following:
http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem
persists for fsaverage, since norm.mgz does not exist for fsaverage. I'm
going to try creating norm.mgz for fsaverage to see if xhemireg works.
Even if it doesn't, xhemireg does work for
why are you running xhemireg for fsaverage?
On 10/02/2012 06:04 PM, Andrew Bock wrote:
> I updated all the xhemi scripts following:
> http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem
> persists for fsaverage, since norm.mgz does not exist for fsaverage.
> I'm going to try c
I have a custom overlay on the left hemisphere of fsaverage, I wanted to
resample that overlay onto the right hemisphere. I thought it would save
time to run xhemireg once for fsaverage, and then resample the left and
right fsaverage overlays onto the left and right hemispheres for all my
subjects
I get a
CUDA error: MRISCcomputeVertexDistances: invalid device function .
during mris_sphere_cuda with a Quadro FX 5600, see the log below, any
advice?:
\n mris_sphere_cuda -q -seed
1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix \n
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 20
Hello everyone,
I am trying to incorporate a binary FMRI mask into mri_glmfit. The
problem is that it does not matter what I put in for the mask file I
get the same results.
This is the command I am using:
mri_glmfit \
--y /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/y.mgh \
--
Hi, don't use --label and --mask.
doug
On 10/2/12 9:15 PM, Brain Apprentice wrote:
> Hello everyone,
>
> I am trying to incorporate a binary FMRI mask into mri_glmfit. The
> problem is that it does not matter what I put in for the mask file I
> get the same results.
>
> This is the command I am u
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