-- Forwarded message --
From: Zhen Zonglei
Date: Tue, Nov 1, 2011 at 11:13 AM
Subject: Position available: Postdoc in System and Cognitive Neuroscience -
Beijing Normal University, China
To: FSL - FMRIB's Software Library
Postdoctoral positions are available to study the neura
Hi David, you can use mri_label2vol with the --proj option. This works
ok, but it is often not great. Another way (the way that aparc+aseg) is
created is to convert your label into an annotation, then use
mri_aparc2aseg.
doug
On 10/31/11 7:22 PM, David Grayson wrote:
> Hi Doug,
>
> Although in
Hi Doug,
Although in principle, yes this is the idea, we have a set of labels that
aren't actually in the aparc+aseg file (basically a set of high-density
subdivisions of those regions). The only problem is that the labels I have are
just in "surface-land." I am wondering, once I have the surfa
Hi Folks
I am using Freesurfer 5.1 and I get the following error: "ERROR:
_FindFacePath: could not find path!"
Is this is a memory related issue ? The same case went through smoothly
with Freesurfer 5.0.
Also I have not seen this error over a large number of subjects and I
thought it might be
hi,
I wonder whether there is a document describing files in surf and label
subfolders in a subject's folder. I wanna know what kind of information is
stored in each of those files.
Cheers, Forrest
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.
In the log file, it says that you did not run it with the -i. Check your
command line.
doug
Chindhuri Selvadurai wrote:
> Hello,
>
> I am having trouble doing a recon-all of my data.
>
> pbsubmit -m chinsel -c 'recon-all -s DODASD001 -all -i
> /cluster/archive/295/siemens/TrioTim-35006-20111026-1
Not from the T1 alone. I wrote a script called intcapseg (it may or may
not be in the distribution). Below is the doc for it. I can get it to
you if you want it, but it is not at all tested or validated.
doug
intcapseg --s subject
--ndil ndil : default is 6
--nero nerodes : default is ndil
I see.
Doug: do you consider this to be a reliably defined white matter region?
If so, would it be possible to to get some information on the tools Bruce
mentioned?
On 10/31/11 4:40 PM, "Bruce Fischl" wrote:
>Doug wrote some tools to do this, but they aren't run by default.
>
>cheers
>Bruce
>On
Hello,
I am having trouble doing a recon-all of my data.
pbsubmit -m chinsel -c 'recon-all -s DODASD001 -all -i
/cluster/archive/295/siemens/TrioTim-35006-20111026-155248-065000/364000-15-01.dcm
-mail chin...@nmr.mgh.harvard.edu'
Here is the error:
ERROR: no run data found in
/autofs/clu
Doug wrote some tools to do this, but they aren't run by default.
cheers
Bruce
On Mon, 31
Oct 2011, Vaidya, Jatin G wrote:
Hi,
We recently processed some T1 data through Freesurfer but I did not see any
labels for the internal capsule. Does Freesurfer still create a label for
this region?
Do you just want the label in the orig volume space? If so, just use the
labels in aparc+aseg.mgz
doug
David Grayson wrote:
> Hi Doug,
>
> /path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label
> lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz
>
> Thanks,
>
> D
Hi,
We recently processed some T1 data through Freesurfer but I did not see any
labels for the internal capsule. Does Freesurfer still create a label for this
region?
Thanks,
Jatin
Notice: This UI Health Care e-mail (including attachments) is covered by the
Hi Doug,
/path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label
lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz
Thanks,
David
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, October 31, 2011 2:04 PM
To: David
what was your label2vol command line?
doug
David Grayson wrote:
>
> Hi freesurfer experts,
>
>
>
> I currently have a set of cortical labels that are the result of a
> high-resolution parcellation of the standard aparc.annot labels (via
> the ‘connectomemapper’ software). I would like to extra
Hi freesurfer experts,
I currently have a set of cortical labels that are the result of a
high-resolution parcellation of the standard aparc.annot labels (via the
‘connectomemapper’ software). I would like to extract the gray matter ROIs that
correspond to these labels, and I understand that th
sorry it didnt work. i figured there was a reason we built with 1.1 and
not 1.0, but forgot what it was (it appears our gpu code requires some
functionality found in 1.1 and newer).
n.
On Mon, 2011-10-31 at 15:36 -0400, Hemant Bokil wrote:
> It was indeed using mri_em_register_cuda. I will check
It was indeed using mri_em_register_cuda. I will check with a different
card. Thanks a lot,
Hemant
On Mon, Oct 31, 2011 at 3:24 PM, Nick Schmansky
wrote:
> which binary was running when this error occurred? consult the
> recon-all.log to find out. if it was mri_em_register_cuda or
> mri_ca_regi
which binary was running when this error occurred? consult the
recon-all.log to find out. if it was mri_em_register_cuda or
mri_ca_register_cuda, then it would appear that it is attempting to use
a function not supported by compute capability 1.0, which means your
card is not supported.
n.
On M
Oops - my bad, on this last round I mixed one filename dash with a dot.
Works now - so (just to remind myself) the new feature is to use
mri_surf2surf to convert from w to mgz before running mri_surfcluster.
Thanks Doug! :) -Tommi
> It looks like that file does not exist:
> ls /autofs/cluster/scr
I don't think so, although you could try it under 5.1 (or send us the
dataset and I'll run it through to see if it turns out any differently)
cheers
Bruce
On
Mon, 31 Oct 2011, Miguel Burgaleta wrote:
>
> Hi Freesurfers,
>
> I'm using FS 4.5.0 to calculate the volume of the corpus callosum, bu
Hi Nick,
Thanks for generating those files. The code ran through more steps this
time (with the new files) but I now have the following error:
Cuda error: MRImeanX kernel failed in file 'mrimean_cuda.cu' in line 578 :
invalid device function.
register_mri: find_optimal_transform
Would you be abl
Your ROI must be listed in the color table, so you'll need to create a
custom color table. For this you will need the ID eventually assigned to
your ROI. To find this out, load the wmparc your created in tkmedit as
both a segmentation and as the aux volume. When you click on your ROI,
the tkmed
Hemant,
We dont have any cards here that are compute capability 1.0. Our test
cards are all 1.3 or higher.
We do compile with -arch sm_11 (compute capability 1.1). I've
recompiled mri_em_register_cuda and mri_ca_register_cuda with -arch
sm_10 and put them here:
https://surfer.nmr.mgh.harvard
On 10/25/11 17:38 , Steph Bickel wrote:
> Hi Rudolph and Bruce,
>
> thanks for your responses.
>
> rudolph, your example works great. just 2 questions:
> what dimension is the total path cost in the mris_pmake output?
> is there a way to input a file with several vertex point pairs to
> compute the
Yes -- the problem is that each 'mris_pmake' instance listens on a
socket. This socket is used for communicating and controlling an
mris_pmake instance that is already running.
If you open multiple 'mris_pmake's they will collide with the "Address
already in use".
How to fix?
Each 'mris_pmake
Hi Freesurfers,
I'm using FS 4.5.0 to calculate the volume of the corpus callosum, but in
about 70% of my subjects (n = 100) I get mild to severe inclusions of the
fornix in the central and/or mid-posterior sections of the CC.
Is there any workaround for this particular issue, before start consid
In general, the software packages don't really care how the data were
acquired (though FSL generally wants images that are in radiological
convention -- check their web site). You do want to make sure that all
your subjects were acquired in the same way (ie, don't acquire some
subjects axially
Dear Freesurfers,
I have a set of MRI data collected in an Axial_T1 and some in Sag3D_T1. I
wonder if after dcm to nii conversion when I get a 3D or 4D volume (if further
use for FSL) it really matter how my data was acquired (Axial or Sag) since the
NIFTI file is in fact a volume. Should I d
It looks like that file does not exist:
ls /autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz
ls: /autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz: No such file
or directory
r...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> I am still receiving a similar error. mri_surf2surf inputes the w fi
Hi Doug,
I am still receiving a similar error. mri_surf2surf inputes the w file
and writes out a mgz file and exits apparently ok. However, mri_volcluster
still exits with
"could not read test-lh.mgz as type"
Details:
mri_surf2surf \
--srcsubject Wyss_000 \
--trgsubject Wyss_000 \
--hemi lh \
-
Hi Alex, I think that is ok.
doug
Alexander Lebedev wrote:
> Dear Freesurfers,
>
> Could you please tell me about your experience with cluster-wise
> correction for multiple comparisons in relatively small samples. For
> instance, is it wise to use CWS for regression with one continuos
> variable
Use mri_segstats. You can look in the recon-all.log file in
subject/scripts. Find the call to mri_segstats used to generate the
wmparc stats, copy it and make the customizations you need.
doug
dolphin...@aol.com wrote:
> Hi Doug,
>
> to get the white matter volume of my ROI-label, i have done th
Hi Tommi, convert the w file to an mgz with mri_surf2surf. Specify the
source format with --sfmt w
doug
r...@nmr.mgh.harvard.edu wrote:
> Hi Doug and Matti,
>
> I am using mri_surfcluster to threshold and extract ROIs from MEG/EEG
> source analysis data. The same code used to work fine in Jan 200
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