Hi all,
I'm sorry if these questions have already been covered here, but I've
looked into the archives and still can't do what I need (and since I'm
running out of time for this task I decided to post here):
I'm using version 5.0.0.
I want to show the resulting Brodmann area (only 3 BA) volu
Dear all,
I am new freesurfer user (version 5.0.0 installed to windows using virtual
machine),
during the installation i was trying to test the installation, following the
recommended steps.
The recon-all -s terminated with errors, andi can't find the bug.
I send you the command line and the re
Hello Anastasia,
It fixed the bug. Thank you so much!
Now Im running trac-all -bedp -c
But it's been running for already 3 days, and it just printed that:
> trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example
INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer
INFO: Diffusion root is
Hi Anthony,
in matlab it would be something like:
vaseg = load_mgh('aseg.mgz') ;
[vmanual,M,mr] = load_mgh('manual_seg.mgz') ;
ind = find(vmanual > 0) ;
vaseg(ind) = vmanual(ind) ;
save_mgh(vaseg, 'manual_seg.with_aseg.mgz', M, mr) ;
cheers
Bruce
On Sun, 22 Apr 2012, Anthony Dick
wrote:
Hi Statos
how much RAM do you have in your machine? It looks like not enough.
cheers
Bruce
On Mon,
23 Apr 2012, Eustratios Karavasilis wrote:
Dear all,
I am new freesurfer user (version 5.0.0 installed to windows using virtual
machine),
during the installation i was trying to test the insta
Hi Andreia
sorry, I don't understand. What do you mean when you say you want to "
show the resulting Brodmann area (only 3 BA) volume in the inflated surface
of my subjects". Do you mean just to show what portion of the surface is in
each of 3 Brodmann areas? That you would do by loading the re
Hi Ruthger
that means that the subject was partially reprocessed but not completed.
You can finish it with:
recon-all -s -sd -make all
cheers
Bruce
On Thu, 19 Apr 2012, Righart, Ruthger Dr. wrote:
> Dear Freesurfers,
>
> I analyzed a dataset with FS 5.1 but upon loading the data in tksurf
for all of prefrontal you mean? No, but it would be easy enough to draw a
label on fsaverage for prefrontal, then map it to every one of your
individual subjects using mri_label2label.
cheers
Bruce
On Thu, 19 Apr 2012, Ahmed, F, Me
wrote:
Hello FS experts,
A quick question for you all. D
Hi,
I'm currently doing a project for my neuroscience course. I've decided to
compare automatic segmentation methods (comparing hippocampus volumes)
(using Freesurfer and FIRST). My question is, whether there is a set of
commands in Freesurfer which will enable me to segment only hippocampus.
I'm o
Hi Pawel
no, sorry, you need to segment everything to get hippocampal volumes. You
can stop after autorecon2 and not run 3, which will save you a bit of time,
but you are probably better off just running them all normally.
cheers
Bruce
On Mon, 23 Apr 2012, Pawe? Dembi?ski wrote:
Hi,
I'm c
(forgot to do answer all, here it goes for the list too)
Citando _andre...@sapo.pt:
> Hi Bruce,
>
> The ideia is to show one control subject vs. one patient inflated
> surface with BA surface (not volume, sorry) to show the difference
> (reduced surface area in one patient). Loading the rele
Hi Erlend, while the images in the tkregister2 pics are oriented
correctly the registration is way off. What images are you loading into
fslview? You'll need to convert the orig.mgz into nii and load that to
check the registration.
doug
On 04/22/2012 04:16 AM, Erlend Hodneland wrote:
> Hi again
Hi Andreia,
yes, they will always shrink since the label contains every point that
could possibly be in the BA, no matter how unlikely. I'll try to find time
to automatically threshold the BAs so that they have the average area of
the individual examples, but for now V2 is probably around .7 an
Hi Koushik, it just uses the label of the maximum.
doug
On 04/19/2012 05:30 PM, Govindarajan, Koushik Athreya wrote:
> Hi,
>
>I have a question regarding how the clusters are labeled after the results
> of a Monte-Carlo Simulation. Similar regions from 2 different patient
> populations seem
Hi Xiangyu, just add --identity fsaverage to the surf2vol command line
doug
On 04/19/2012 05:57 PM, Long wrote:
> Hi all,
>
> I had a question when convert a surface to volume space.
>
> First, I converted a volume nifti data to fsaverage:
>
> mris_preproc --target fsaverage --hemi lh --iv data
Hi Doug,I'm running the FS v5.1 under centOS 4.3 and after changing the mri_segstats you send me, i always get the following error message:mri_segstats: /lib64/tls/lib.so.6: version 'GLIBC_2.4' not found (required for mri_segstats).Does this is normal, since the same FS version was running perfectl
Hi Gabriel, I'll need to wait for Nick or Krish to respond to this one.
N/K: I'm trying to give Gabriel a new version of mri_segstats that I
compiled on Linux tanha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25
EST 2011 x86_64 x86_64 x86_64 GNU/Linux
doug
On 04/23/2012 10:35 AM, Gabriel Gonzale
Gabriel:
try running ldd on the mri_segstats and see what libraries it is trying
to find and whether you have them all.
cheers
Bruce
On Mon, 23 Apr 2012, Douglas N Greve
wrote:
Hi Gabriel, I'll need to wait for Nick or Krish to respond to this one.
N/K: I'm trying to give Gabriel a new ver
I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro
running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the Ubuntu
virtual machine package provided for Windows (OS was Windows XP).
I'm going to attempt run the command exactly as you wrote it in the e-mail to
can you try it on a linux machine?
On Mon, 23 Apr 2012, Andrew C Yourich
wrote:
> I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro
> running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the
> Ubuntu virtual machine package provided for Windows (OS was Wind
I personally do not have access to a Linux machine, but I do know someone in
our department that does run freesurfer on one. I had e-mailed him on Friday to
see if he encountered this issue as well, so let me follow up with him and see
if he is able to check mris_expand results on his computer.
Dear Freesurfer list,
I am using optseq2 for the first time and wanted to check with you whether my
protocol makes sense, many thanks in advance for your insight.
1) I start by choosing the maximum scan duration equalling ~30 min:
2) set the psd window so it can capture the entire waveform of a
Hi Douglas,
I tried to do spatial normalization for volume data, all steps are
following:
1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s subj01
--init-fsl --reg bb_register.dat
I checked the result by tkregister2, it looked good.
2) mris_preproc --target fsaverage --hemi lh --iv fsu
hi Lilla,
I ended up with the same error... so I'm not sure what else to try. Do
you have an ideas for troubleshooting?
I've also attached the latest log file, although it's probably very similar
to the first one.
thanks,
jackie
On Fri, Apr 20, 2012 at 6:10 PM, Jackie Leung <
jackie.le...@alu
Hi Jackie,
Sorry that the error is still there. Are you sure that the attached log
file is for the below command? I am asking as the log file indicates that
spherical registration is done and that should not happen in Step2.
Also, could you tell me which version of the FS distribution you ar
Hello,
We are getting the following error while processing T1 data acquired
on Philips. The image data looks ok. We have three scans with similar
error. Does anyone have suggestions as to what could be wrong?
Loading pixel data
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::
(sorry, here it is for the list again)
- Mensagem encaminhada de Bruce Fischl -
Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT)
De: Bruce Fischl
Assunto: Re: [Freesurfer] Load Brodmann surface area into inflated surface
Para: _andre...@sapo.pt
Hi Andreia,
can you cc the lis
Hi Betina, see answers below
doug
On 04/23/2012 12:04 PM, Betina Ip wrote:
> Dear Freesurfer list,
>
> I am using optseq2 for the first time and wanted to check with you whether my
> protocol makes sense, many thanks in advance for your insight.
>
> 1) I start by choosing the maximum scan duratio
Is this one of the new dicom format files? The new ones have a single
dicom file with all the pixel data in it (and we can't read them yet).
doug
On 04/23/2012 03:22 PM, Mohana Ramaratnam wrote:
> Hello,
>
> We are getting the following error while processing T1 data acquired
> on Philips. The im
Hello,
Thank you Michael for your input. My feeling was that surface area would
scale with ICV. In any case, is there any recommendation on how to
normalize the Jacobian? My other ramble is that since it is already mapped
into a common space, would I normalize the Jacobian, or would I have to
n
Hi Freesurfers,
I just want to check my observation that Freeview can not currently be used
for editing the WM.mgz or the brainmask.mgz (for minor skull strip errors)
as is done in TKmedit (cf., Edit Tutorial). Is that correct?
I can’t find any documentation on this, and whilst I would assume
Hi All,
When we do the GroupAnalysis,there is a vector(such as: 0 0 0.5 0.5).And I
just want to know how this vector involve in calculating?
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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So shorlty after I sent that email I figured out how to do a little of what
I spoke about...
a) White matter (WM.mgz) edits - joining WM fingers in the WM.mgz or
filling holes, etc..Should New WM voxels in WM.mgz should be = 255
(brush value)??
b) I can delete skull/dura..should I be repl
It's hard to say without more information, but that looks like a
contrast vector which is used to test a hypothesis.
On 4/23/12 9:00 PM, bowan...@mail.ustc.edu.cn wrote:
> Hi All,
> When we do the GroupAnalysis,there is a vector(such as: 0 0 0.5 0.5).And
> I just want to know how this vector
Why do you want the jacobian? The surface area is a more interpretable
measure. If you use surface area, make sure you get the patch for
mris_preproc.
doug
On 4/23/12 8:07 PM, Jeff Sadino wrote:
Hello,
Thank you Michael for your input. My feeling was that surface area
would scale with ICV.
Dear all,
I want to use N3 on nifti images, and I have different versions installed on
two machines.
On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert
version 4 and everything works fine.
On the other machine I have N3 version 1.12 which uses mri_convert version 5;
th
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