Hi Folks,
I am running recon-all with -autorecon1 -autorecon2, -nomotioncor
-notal-check -nonuintensitycor
(this is with fs version 5.3)
it almost runs through but toward the end, when mri_segstats is called I
get the error message:
.../mri/ribbon.mgz, -1): could not open file
any ideas why this
ps: i believe my error is the same as the one in this thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html
Mehul
On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat mpsam...@gmail.com wrote:
Hi Folks,
I am running recon-all with -autorecon1 -autorecon2, -nomotioncor
Hi Freesurfers,
I'm trying to remove some dura which affect my surfaces with the command
recon-all -skullstrip -clean-bm -gcut -subjid
but then I can't use tkmedit to check that.
The message I get is:
Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical
volume. Tkmedit
Dear FS experts,
I have a problem with the command recon-all.
In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING
INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are
killed at the command nu_currect, as you can see from the file.log in
Hi Freesurfers!
I'd like to load my original Nifti T1 image data (subject.nii) and the
wm/gm-surface coordinate data (for instance lh.pial) in matlab as vectors
in the same coordinate system.
If I do it in the naive way,
i.e. [x,y,z,1]=[i,j,k,1]*sform' for the Nifti coordinates resp.
did you run out of disk space? Can you run mri_info on it?
On Thu, 30 May
2013, Claudia Dacquino wrote:
Hi Freesurfers,I'm trying to remove some dura which affect my surfaces with
the command
recon-all -skullstrip -clean-bm -gcut -subjid
but then I can't use tkmedit to check that.
The
Yes I did run mri_info, these are the results:
Volume information for brainmask.gcuts.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1., 1., 1.
type: INT (1)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
is your disk partition full? And please cc the list so others can answer
Bruce
On
Thu, 30 May 2013, Claudia Dacquino wrote:
Yes I did run mri_info, these are the results:
Volume information for brainmask.gcuts.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.,
yes I did answer again to the list.
no it is no full at all.
2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu
is your disk partition full? And please cc the list so others can answer
Bruce
On Thu, 30 May 2013, Claudia Dacquino wrote:
Yes I did run mri_info, these are the results:
Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz will
not get created till autorecon3. In V4, that is part of autorecon2 though.
Gen
On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat mpsam...@gmail.com wrote:
ps: i believe my error is the same as the one in this thread:
Could you provide the recon-all.log file?
-Zeke
On 05/30/2013 10:24 AM, Gennan Chen wrote:
Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz
will not get created till autorecon3. In V4, that is part of autorecon2
though.
Gen
On Thu, May 30, 2013 at 12:24 AM, Mehul
and my freesurfer version is 5.1.
2013/5/30 Claudia Dacquino claudia.dacqu...@gmail.com
yes I did answer again to the list.
no it is no full at all.
2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu
is your disk partition full? And please cc the list so others can answer
Bruce
On
I am running version 5.3- the latest version. I also tried running the codes on
v5.0 and got the same result. Is there any way I can change the color table so
that the colors of the parcellation are unique?
Thanks,
Tina
-Original Message-
From: Bruce Fischl
It is probably the region that is more than 5mm away from cortex. In the
wmparc it should be labeled as wm-lh-unknown
doug
On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote:
Hi Doug:
I used the instructions that you told me to get the white matter per
each lobule... But, I got the grey
Hi Subha, use mri_segstats, something like
mri_segstats --i norm.mgz -seg arcfas.mgz -id 1 -sum arcfas.summary.dat
Look at the --help for more info
doug
On 05/30/2013 07:04 AM, Subhabrata Chaudhury wrote:
Hello Everyone,
Greetings.
I am learning freesurfer tricks. I am stuck and have a
Hi Max, does this page give you what you need to know?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 05/30/2013 08:29 AM, schre...@informatik.hu-berlin.de wrote:
Hi Freesurfers!
I'd like to load my original Nifti T1 image data (subject.nii) and the
wm/gm-surface coordinate
Hey Doug,
I was wondering whether you had a chance to give this a look!
Thanks again,
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
Sent: Tuesday, May 28, 2013 1:38 PM
To:
Hi all,
This is a follow-up on my question so that people can know what I've tried
and how it works. I added control points in the white matter and the
delineation of the temporal lobe has improved to a satisfying level. We
also find what Michael has suggested very interesting. But it seems that
Jon,
I have not seen or heard of this error before... are both machines Mac
OSX 10.6.8? Also, will the same command will produce a brain image when
not logged in remotely?
-Zeke
On 05/30/2013 12:43 PM, Jon Wieser wrote:
hi freesurfer folks
I'm ssh'ing to from one MAc to another
X11 is
Hello everyone,
I just updated to Freesurfer 5.3.0, my OS is Ubuntu 12.04. When I run
'recon-all -i T1 image -subjid subject name' I receive the following
error:
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
The directory structure appears to be set up correctly, and the
Hello all, I seem to be having some difficulty downloading the freesurfer
software to my MAC computers. I have tried my laptop (MacBook pro, I don't
remember the version but it is approx. 10.3) as well as a desktop (imac,
mac osx version 10.8.3) and also tried two different networks. I have
Hi Andrew,
It is expected that you would not see this warning with Freesurfer
version 5.1.
Its just a warning, but tcsh v6.17.06 on Ubuntu always returns exit code
0. This can be problematic for instances where recon-all encounters and
error and should fail. If you ran recon-all and have all
Mike,
I just tested the links on this page the download page and they work for me:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
What happens when you type this command into your terminal:
curl -O
Thanks Zeke.
To my knowledge tcsh v6.17.06 is the latest version of tcsh for Ubuntu
12.04 LTS, but I just discovered tcsh v6.18.01 is available for more recent
versions of Ubuntu (e.g. Ubuntu 12.10, 13.04). If you (or anyone else)
knows of any issues with tcsh v6.18.01 please let me know,
Hi!
Is there more documentation on what settings the mprage flag enables in
recon-all?
Specifically, I would be interested which individual steps it affects and
what the parameters are for each of the steps.
Thanks!
Caspar
___
Freesurfer mailing list
Hi Doug:
But, in the mri_aparc2aseg command, I test with the --wmparc-dmax
200 option... I put that big value to test it, but I got the image
that I sent you...
Sincerely,
Gonzalo Rojas Costa
On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
It is
both machines have Mac OS X 10.6.8
the tkmedit works fine when not logged in remotely
there is no error and the brain image is there
Jon
- Original Message -
From: Z K zkauf...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Thursday,
Hello Freesurfer users
I'm trying to replicate my earlier findings in 3D space by warping the data
into surface using freesurfer.
Previously, the 3D data were smoothed using 4mm FWHM kernel and I'm
wondering what size of smoothing kernel for 2D would be equivalent to 4mm
for volumes.
Any help
there is no equivalent. I'd start with 4 and move up.
doug
On 05/30/2013 02:51 PM, Glen Lee wrote:
Hello Freesurfer users
I'm trying to replicate my earlier findings in 3D space by warping the
data into surface using freesurfer.
Previously, the 3D data were smoothed using 4mm FWHM kernel
Yes it worked. Thank you that is exactly what I needed.
Tina
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 12:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Tina Jeon
Subject: Re: [Freesurfer] mris_divide_parcellation color table
Hi Glen
there is no way to get an equivalent 2D kernel to the 3D one.
sorry
Bruce
On Thu, 30 May 2013, Glen Lee
wrote:
Hello Freesurfer users
I'm trying to replicate my earlier findings in 3D space by warping the data
into surface using freesurfer.
Previously, the 3D data were
hmm, can't tell from that what is going on. Can you tar up
lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
the end of this email)?
doug
On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
Hey Doug,
Of course, I attached it in txt format in this email!
Best,
Panos
can you send me your full command line as well as the terminal output?
On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:
Hi Doug:
But, in the mri_aparc2aseg command, I test with the --wmparc-dmax
200 option... I put that big value to test it, but I got the image
that I sent you...
Definitely, just uploaded it!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:10 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
hmm,
On Thu, May 30, 2013 at 2:37 PM, Jon Wieser wie...@uwm.edu wrote:
both machines have Mac OS X 10.6.8
the tkmedit works fine when not logged in remotely
there is no error and the brain image is there
Did you do ssh -Y or have ForwardX11Trusted yes in your ssh.config?
Richard
This is a problem with version 5.0 when you set the clusterwise pvalue
to something close to 1. I re-rand it with .995 and it work. This is
fixed in 5.3
doug
On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote:
Definitely, just uploaded it!
Panos
Hi Doug:
The command is:
mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200
and the terminal output is:
mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
--volmask --o
Hi,
I have an experiment where I have 3 conditions in a FIR event related
analysis (running FS 4.5). I need to get the mean activity level for each
voxel across all conditions across the run, so that I can calculate percent
signal change for each individual voxel. Is this available (I have
Just to make sure I'm doing this right, I'm going to summarize what I've taken
away from your answers and to ask some new questions. In order to present the
results, I need two things:
1) A set of histograms (with error bars) for each cluster figure to show the %
signal change for each of the
Great, thanks!!
In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis
on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I
still need to apply the correction over the two hemispheres (that is divide by
2 the cluster wise threshold since in FS 5.0.0
yes
On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote:
Great, thanks!!
In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis
on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I
still need to apply the correction over the two hemispheres (that
Hi Katie, I don't remember what 4.5 outputs. Is there a meanfunc
volume there? Itwould be much easier to support you if you were using
version 5.x:)
doug
On 05/30/2013 04:36 PM, Katie Bettencourt wrote:
Hi,
I have an experiment where I have 3 conditions in a FIR event related
analysis
Great, thanks!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:47 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
yes
On 05/30/2013
yes,
I have ForwardX11Trusted yes in ssh_config
and I do ssh -Y
Jon
- Original Message -
From: R Edgar freesurfer@gmail.com
To: Jon Wieser wie...@uwm.edu
Cc: Z K zkauf...@nmr.mgh.harvard.edu, freesurfer
freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, May 30, 2013 3:26:05 PM
Subject:
I tried using MRIread to look at the contents of the analysis files (using
Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol:
Sorry for the follow up email. If for instance I want to see any clusters that
have a p value of 0.05 or less, I need to set the cluster wise p value in the
mri_glmfit-sim command to 0.025 (to account for the correction over the two
hemispheres). Then, suppose that a cluster is shown in the
Hi All,
Is there a way to combine multiple binary volumetric masks into a single binary
volumetric mask in freesurfer ?
Please let me know.
Thankyou
Subha
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
That is a surface file. Each of the 163842 values corresponds to a
vertex in the surface. If you want xyz, you need to load in the surface.
You can also analyze the data in the native space if that would make it
easier (but you can't surface smooth).
doug
On 05/30/2013 05:08 PM, Joseph Dien
you would report .03
doug
On 05/30/2013 05:10 PM, Fotiadis, Panagiotis wrote:
Sorry for the follow up email. If for instance I want to see any clusters
that have a p value of 0.05 or less, I need to set the cluster wise p value
in the mri_glmfit-sim command to 0.025 (to account for the
you can use
fscalc mask1.mgh and mask2.mgh -o mask1-and-mask2.mgz
assuming you want to use an AND function
doug
On 05/30/2013 05:18 PM, Subhabrata Chaudhury wrote:
Hi All,
Is there a way to combine multiple binary volumetric masks into a
single binary volumetric mask in freesurfer ?
Please
Oh duh. Okay, thanks!
Joe
On May 30, 2013, at 5:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
That is a surface file. Each of the 163842 values corresponds to a vertex in
the surface. If you want xyz, you need to load in the surface. You can also
analyze the data in the native
Hello Doug,
Thank you. Will fscalc work with volume mask ? You wrote .mgh. mgh is surface
data, right ?
Best wishes
Subha
- Original Message -
From: Douglas N Greve
Sent: 05/30/13 05:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] combining masks in freesurfer ??
you
mgh format can be volume or surface. fscalc will work with either. it
will also work with nifti or analize formats
On 05/30/2013 05:44 PM, Subhabrata Chaudhury wrote:
Hello Doug,
Thank you. Will fscalc work with volume mask ? You wrote .mgh. mgh is
surface data, right ?
Best wishes
Subha
Mike,
I have tested the download from multiple computers on multiple different
networks, including my home network. It is successful everytime. I dont
know if you have a a system administrator who can help resolve the
situation on your end but everything seems to be running correctly on our
side.
Hi Subha
you could use mri_and to do the job
cheers
Bruce
On Thu, 30 May 2013, Subhabrata
Chaudhury wrote:
Hi All,
Is there a way to combine multiple binary volumetric masks into a single
binary volumetric mask in freesurfer ?
Please let me know.
Thankyou
Subha
Hi Mia
That's a very large defect. Can you visualize it and see if you can figure out
where it comes from?
Bruce
On May 30, 2013, at 2:39 PM, Borzello, Mia mborze...@partners.org wrote:
Hi freesurfers,
I encountered an error using recon-all for a scan series of 177 slices. I'm
not sure
Hi all, probably mostly Bruce and co.,
I've just got a new linux box set up and am able to run all graphical tools and
recon-all OK.
Linux Mint 15 x64 RC (based on Ubuntu 13)
Intel i5 Ivy Bridge
nVidia GTX 650 Ti
nVidia drivers: Selected from System Device Drivers; nvidia-313-updates;
I was able to make more progress so I'm mostly good at this point but I have a
remaining question:
I assume the contents of sig.nii.gz (which I assume are the vertex p-values)
are not FWE corrected. Is it possible to get FWE-corrected vertex p-values?
Or are only clusterwise corrections
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