edu> escreveu:
> Which version of FS are you using? I don't have this problem in v6 or dev.
> What OS are you using?
>
>
> On 1/17/2020 9:09 AM, Marcos Martins da Silva wrote:
>
> External Email - Use Caution
> Thank you, Doug! Yes, there is an option to load a fs
eview
>
> On 1/15/2020 11:02 AM, Marcos Martins da Silva wrote:
>
> External Email - Use Caution
> Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with
> input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click
> inside the box a
External Email - Use Caution
Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with
input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click
inside the box and even select the content but it seems read only: I can't
change it. So it is impossible
Hi, Greg
I use to process my subjects with:
recon-all -s subjid -all -hippo-subfields
The -all flag makes the program run all the 3 stages (autorecon1,
autorecon2 and autorecon3) in sequence. Only after this it starts the
hippo-subfields stage. If you do not have any special reason to run each
au
Hi, Joshua
Just answered this to Mohammad Zia in a previous message and I guess it
is useful to you.
1- The name "Right-Hippocampus" is misleading you. The hippocampal
subfields segmentation is atlas based. And the atlas was generated from
expert manual segmentation. The problem is that the most
Hi, Zia
1- The name "Right-Hippocampus" is misleading you. The hippocampal
subfields segmentation is atlas based. And the atlas was generated from
expert manual segmentation. The problem is that the most posterior part
of hippocampal tail is too small to allow a precise segmentation. So
they know i
ading the label. Then try loading
> >> LeftHippoBody_surf.mgh. If that does not look ok, check the registration
> >> between binLeftHippoBody.mgz and subj1 with --regheader
> >>
> >> doug
> >>
> >> On 10/24/2013 06:40 PM, Marcos Martins da Silva wro
oading
> LeftHippoBody_surf.mgh. If that does not look ok, check the registration
> between binLeftHippoBody.mgz and subj1 with --regheader
>
> doug
>
> On 10/24/2013 06:40 PM, Marcos Martins da Silva wrote:
> > Hi, Doug
> > Thanks again for your help.
> > Using the com
Hi, Douglas
Just to check if I correctly understood you, when you said
"mri_label2vol can go in both directions" did you mean it can also
create a label from a volume or a binary mask? If so, could you please
explain how? I read documentation on wiki and help from the command
itself and could not s
em, which is a bug in one of the open source math
> libraries we use. If you email us the details of your hardware/software
> environment we'll get you a patch.
>
> cheers
> Bruce
> On Mon, 7 Oct 2013, Marcos Martins da
> Silva wrote:
>
> > Hi
ompleted as unzip can't find the end of directory
> mark in the file. Try our filedrop instead:
>
> https://gate.nmr.mgh.harvard.edu/filedrop2/
>
> cheers
> Bruce
>
>
> On
> Mon, 7 Oct 2013, Marcos Martins da
> Silva wrote:
>
>
ack it down
> On
> Mon, 7 Oct 2013, Marcos Martins da Silva wrote:
>
> > Hi, Bruce.
> > Thank you for your fast answer.
> > I used a script and It took less than 15 min to process all files from all
> > subjects, except
> > the 3 files (surfaces) mris_sm
attention.
2013/10/4 Bruce Fischl
> how long have you waited?
>
>
> On Fri, 4 Oct 2013, Marcos Martins da Silva wrote:
>
>
>> Hi, Freesurfers
>> I am getting some interesting hippocampal surfaces with the following
>> steps:
>> 1- recon-all -all -hippo-
You can use in a loop with your subjects. It extracts the fields I want
and some others including the etiv to a table named AsegVol. You may
change the number of the fields to get what you need. The code I am
sending you addresses hippocampus, putamen and caudate (both sides).
te surface for subcortical
> structures from individuals. I think FSL might do this kind of thing.
> doug
>
>
>
>
> On 08/07/2013 04:03 PM, Marcos Martins da Silva wrote:
> > Hi, FreeSurfers.
> > Is it possible to use FreeSurfer's group analysis tool
Hi, FreeSurfers.
Is it possible to use FreeSurfer's group analysis tools to investigate
surface deformation instead of thickness? I guess it would be
interesting for subcortical structures like putamen, amygdala or
hippocampus. Let's say you get the putamen data from 15 subjects and
compare it to p
Hi, Rune and Zeke
I have posted some time ago my experience with VirtualBox. I also got
similar segfaults. The only way I could run FreeSurfer without problems
was installing CentOS64 on a second hard disk so I have a dual boot
system and skipped VirtualBox. Freesurfer 5.3 also solved some proble
Dear, Zoe
Usually after Freesurfer fresh install you will get a SUBJECTS_DIR with
several directories, including Bert. The script you used will scan all
directories under SUBJECTS_DIR and if it finds any directory without the
posterior*.mgz files it will fail. You can check if this is the problem
r
the posterior*.mgz does not have that
> info. Maybe Koen or Eugenio know why. In the mean time, you can use
> mri_convert to change/set the parameters, eg
>
> mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
>
> doug
>
>
>
>
>
>
> On 6/18
e/set the parameters, eg
>
> mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
>
> doug
>
>
>
>
>
>
> On 6/18/13 2:50 PM, Marcos Martins da Silva wrote:
>
> >
> > Hi, Freesurfer experts
> > If you try to read one of the posterior*.
Hi, Freesurfer experts
If you try to read one of the posterior*.mgz files generated by reco-all
-hippo-subfield into MatLab/Octave using MRIread.m it fails like this:
Ps=MRIread('posterior_left_subiculum.mgz')
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bound
gt; > at different levels of processing. What the best measure is depends on
> > what you want to do with them.
> > Cheers,
> > /Eugenio
> >
> > On Tue, 2013-06-11 at 11:46 -0300, Marcos Martins da Silva wrote:
> > > Hi, Eugenio,
> > > TY again for
u want to do with them.
> Cheers,
> /Eugenio
>
> On Tue, 2013-06-11 at 11:46 -0300, Marcos Martins da Silva wrote:
> > Hi, Eugenio,
> > TY again for your help. I did the computing without errors after your
> > suggestions. I also computed the intensities based on nu.
mean=sum(data.*post)/sum(post);
> variance=sum((data-mean).^2.*post)/sum(post);
> Cheers,
> /Eugenio
>
> On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
> > Hi, Eugenio
> > TY for your fast help. I understood you were suggesting to compute
> > that on
Hi, Freesurfer Experts
After usual processing with recon-all -all we get the aseg.stats file
with several data including intensity values like:
normMean normStdDev
normMin normMax normRange
Left-Hippocampus 77.8939 7.574846.0
I usually use this little bash script (named myrecon) to process my
images.
#!/bin/bash
mkdir ~/freesurfer/subjects/$1/mri/orig -p
cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/
recon-all -all -s $1 -cw256 -hippo-subfields -qcache
With this script I get the entire -all pipeline
Kristina,
I do not know what virtual machine manager you intend to use. If you
will use Oracle's VirtualBox I would like to share my recent experience
with you. I tried a updated CentOS6 virtual machine with Freesurfer 5.2
running under Fedora 18 as host but I had problems during recon-all
tests. I
> On Thu, May 16, 2013 6:22 pm, Marcos Martins da Silva wrote:
> >
> > Hi, Doug
> > Thank you for your answer.
> > Well I guess that after I read your both tutorials for group analysis
> > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and
>
we do with cortical data.
Cheers,
Marcos
Em Qui, 2013-05-16 às 11:56 -0400, Douglas N Greve escreveu:
> Hi Marcos,
>
>
> On 05/15/2013 08:32 PM, Marcos Martins da Silva wrote:
> > Hi, freesurfers
> > I have two questions:
> > 1- Is there a way to use QDEC to analyze data
Hi, freesurfers
I have two questions:
1- Is there a way to use QDEC to analyze data from hippocampal subfields
created by recon-all -s subj -hippo-subfields? That is, I know I can
manually put data from posterior* files when making the FSGD file but it
would be great if I could import it like I do
Hi, all
I have just finnished my FS 5.3-Beta recon-all test in Fedora 18 and
compared to FS 5.2 in CentOS6. Both OS are installed in the same machine
but different HDs.
I used recon-all -all -hippo-subfield in the same subject for both runs
and it worked great. The time in both versions were simil
Hi, Nick.
Recently, you sent me a test version of tkmedit to test under Fedora 18
to address the glibc problem. That tkmedit worked great and you said we
would have a new version of the whole package in brief. Is this 5.3 BETA
the versio addressing this glibc problem?
Em Sex, 2013-05-03 às 17:46
That is the same error I got when using Fedora 18 and should be due to
the newest version of glibc.
Em Qui, 2013-05-02 às 11:46 -0400, Nick Schmansky escreveu:
> Joerg,
>
> Later this evening or tomorrow we'll post a beta that has the fixes for
> this problem for you to try on Ubuntu. When its r
n divide the
> > hippocampus up along the primary eigenvector
> >
> > cheers
> > Bruce
> > On Thu, 18 Apr 2013, Marcos
> > Martins da Silva wrote:
> >
> > > Thank you for your answer, Juan.
> > >
> > > Yes, I want a surface of the
Thank you for your answer, Juan.
Yes, I want a surface of the whole hippocampus and I thought I had just
obtained that using freeview and adding all hippo-subfield files. That
resulted in the screenshot I previously attached. I just do not know how I
can save the resultant surface.
After I check
I had several problems testing freesurfer 5.2 installation, as
previously posted. Now it is all OK and I would like to share what I
could learn:
1- It does not work on Fedora 18 (segfaults with all tests with tkmedit,
tksurfer and recon-all) that is due to a restriction imposed by glibc
(only ne
I had several problems testing freesurfer 5.2 installation, as
previously posted. Now it is all OK and I would like to share what I
could learn:
1- It does not work on Fedora 18 (segfaults with all tests with tkmedit,
tksurfer and recon-all) that is due to a restriction imposed by glibc
(only new
Hi, I can confirm the problem with Fedora 18 is that former glibc version
would accept unsupported salt values, but newer versions
of the library have become stricter. More details at
https://bugzilla.redhat.com/show_bug.cgi?id=905638
I can also say you can run tkmedit, tksurfer and freeview if yo
Hi, freesurferers
I am trying to execute the post installation tests as recommended at
Freesurfer Wiki.
Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over
Fedora 18 using VirtualBox 4.2.8. Freesurfer version is 5.2. Tkmedit,
Tksurfer, qdec and freeview all work great. However,
Hi, freesurfers
I am trying to execute the post installation tests as recommended at
freesurfers website.
Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over
Fedora 18 using VirtualBox 4.2.8. Tkmedit, Tksurfer, qdec and freeview all
work great. But recon-all tests return errors
I installed virtualbox 4.2.8 and CentOS6 (kernel
2.6.32-358.2.1.el6.x86_64). Got tkmedit and tksurfer working on CentOS VM.
Recon-all starts and run for sometime but stop with errors a bit later. On
bright side I noticed freeview works great both on centos VM and on Fedora
18. At your site, I read
I did and got the following to test freesurfer installation according to
freesurfer website directions:
[marcos@alien ~]$ tkmedit bert orig.mgz
===
ERROR: A segfault has occurred. This is not your fault,
: but is most likely an unrecoverable error and has
: mad
42 matches
Mail list logo
