hi folks,
are there predefined mappings between the fsaverage surfaces? for example,
i have an array of numbers for all the vertices in fsaverage4. is there an
easy way to map those to vertices on to fsaverage/fsaverage5/... without
going through surf2surf? something perhaps implemented in matlab
hi dan,
if you use bbregister to match the DTI b0 to freesurfer space, then you can
transform the surface back (no guarantees on the tesselations though i
think). the only additional component here would be a tkr transform that's
based on the conformed space. i might even have some python code
For details of the position and for applying see:
http://sh.webhire.com/servlet/av/jd?ai=631ji=2681168sn=I
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The information in this
hi anastasia,
i'm trying to debug a seg fault that some folks are seeing deep into a
tracula run.
process:
1. feed dicoms to a script that runs DTIPrep and outputs a nifti file,
bvec, bval
(among checking for many artifacts, this reduces the b=0 volumes to a
single registered mean volume, runs
. (Assuming the data
was acquired with the standard Siemens 60 gradient directions.)
a.y
On Tue, 2 Jul 2013, Satrajit Ghosh wrote:
hi ay,
i'll look into the orientations a little later tonight, but here is V1
overlaid on FA for preflip and postflip execution of dtifit.
cheers,
satra
hi bruce and others:
i'm getting a recon failure on this particular brain: H0351.1009
the quality isn't great, but if you can take a quick look at the brain to
see if you can spot any particular issues, that would be great.
4 of the others finished recon and 3 are almost there.
cheers,
satra
hi doug,
bbregister was running into an error trying to do T2pial refinement
sequence of commands and output here:
https://gist.github.com/satra/5934639
and it looks like the absence of FSLDIR
i didn't have FSL installed on this machine - i thought that freesurfer had
it's own version of
.
cheers
Bruce
On Fri, 5 Jul 2013, Satrajit Ghosh wrote:
hi bruce and others:
i'm getting a recon failure on this particular brain: H0351.1009
the quality isn't great, but if you can take a quick look at the brain to
see if you can spot any particular issues, that would be great.
4
here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
doug
On 07/05/2013 09:55 AM, Satrajit Ghosh wrote:
hi doug,
bbregister was running into an error trying to do T2pial refinement
sequence of commands and output here:
https://gist.github.com/satra
ERROR: cannot find $FSLDIR/etc/flirtsch/xyztrans.sch
exit 1;
endif
endif
```
cheers,
satra
On Fri, Jul 5, 2013 at 1:05 PM, Satrajit Ghosh sa...@mit.edu wrote:
thanks doug, i'll try that version right now.
cheers,
satra
On Fri, Jul 5, 2013 at 11:37 AM, Douglas N Greve
gr
/05/2013 01:29 PM, Satrajit Ghosh wrote:
hi doug,
same error with the updated one when i don't have FSL installed.
writing to /data/subjects/H0351.2002/mri/**transforms/tmp.bbregister.**
7856/template.nii...
fslregister --s H0351.2002 --mov /data/subjects/H0351.2002/mri/**
transforms
hi,
trying to figure out the likelihood of identical subcortical volumes across
individuals. i'm noticing this in some data processed with FreeSurfer 5.1.0.
just to give some probabilities - these are out of about 963 participants.
and there are several such small clusters of identical numbers
, 2013 at 1:07 PM, Satrajit Ghosh sa...@mit.edu wrote:
hi,
trying to figure out the likelihood of identical subcortical volumes
across individuals. i'm noticing this in some data processed with
FreeSurfer 5.1.0.
just to give some probabilities - these are out of about 963 participants
...@nmr.mgh.harvard.eduwrote:
Hi Satra
this seems vanishingly unlikely to me, particularly with partial volume
correction. Have you visualize some of the subjects that have the same
structure volume?
Bruce
On Mon, 8 Jul 2013, Satrajit Ghosh wrote:
a quick update. the following fiddle will show
hi sebastian,
please take a look at pysurfer (https://github.com/nipy/pysurfer) and
nibabel (https://github.com/nipy/nibabel).
the relevant code is here:
https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py
cheers,
satra
On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs
hi bruce,
related to this question, how are the stats/volumes of the BAs computed?
cheers,
satra
On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Laouchedi
that is a big research question! The answer is a qualified yes, but it
depends strongly on what
a thresholded
version in 5.3, but perhaps she can comment.
Bruce
On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
hi bruce,
related to this question, how are the stats/volumes of the BAs computed?
cheers,
satra
On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote
...@nmr.mgh.harvard.edu wrote:
There is a *.thresh.label version of all the BA labels in 5.3, but I don't
think it's used by default. You can try using those labels instead.
On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
hi bruce,
currently 5.3, but the data i was looking at was processed with 5.1
hi sarah,
you'll get a much quicker response posting PySurfer related questions to:
nipy-de...@neuroimaging.scipy.org
cheers,
satra
On Fri, Jul 26, 2013 at 12:57 PM, sar...@nmr.mgh.harvard.edu wrote:
Hello Freesurfer Experts,
We would like to use PySurfer's function plot_label_foci.py to
hi folks,
i'm using mri_vol2surf to map functional time series into fsaverage3/4. my
assumption is that each vertex time series will be the mean over an
icosahedral patch corresponding to the vertex on fsaverage. is that how the
resampling is done? also is the resampling done with a single
thanks very much doug.
cheers,
satra
On Tue, Oct 8, 2013 at 11:55 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
On 10/08/2013 09:17 AM, Satrajit Ghosh wrote:
hi folks,
i'm using mri_vol2surf to map functional time series into
fsaverage3/4. my assumption is that each vertex time
hi
i noticed a big discrepancy in size between these two, but not among other
lh and rh gcs files.
28769857 May 13 17:21 rh.DKTatlas100.gcs
6883965 May 13 17:21 lh.DKTatlas100.gcs
are these the intended sizes?
this is from the 5.3 centos6_x86_64 distro
cheers,
satra
, 2013 at 5:11 PM, Satrajit Ghosh sa...@mit.edu wrote:
hi folks,
has anybody on this list:
a. built or extracted the necessary pieces (binaries, libraries, atlases)
for running vanilla recon-all only?
b. or better still, has a package file for any linux distro? i know the
neurodebian folks
hi doug,
could you please highlight the changes - especially if there are any
critical bug fixes? and should we rerun the new mri_segstats on our current
5.3 processed data?
cheers,
satra
On Mon, Nov 4, 2013 at 9:26 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
I've put new versions
, then there is not a problem. If you run
recon-all partially, then it may fail because it runs mri_segstats before
the ribbon.mgz is created.
doug
On 11/04/2013 09:30 AM, Satrajit Ghosh wrote:
hi doug,
could you please highlight the changes - especially if there are any
critical bug fixes
hi martin,
if you had one region you can use mri_segstats to extract for each voxel in
that roi, but not for multiple rois.
here is a snippet i use for timecourses in each roi.
https://github.com/nipy/nipype/blob/master/examples/rsfmri_preprocessing.py#L219
cheers,
satra
On Tue, Nov 5, 2013
Does Freesurfer's GPU bits care about single or double precision?
Cheers, satra
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hi a.y.,
when running trac-preproc i'm getting this error (for dmri_motion and
dmri_group), but it continues running:
/software/freesurfer/bin/dmri_motion: error while loading shared libraries:
libnetcdf.so.6: cannot open shared object file: No such file or directory
what will this fail to do?
update: the lack of libnetcdf eventually makes it fail.
i found a libnetcdf.so.7 on the cluster and soft linked it to
libnetcdf.so.6 and added the path to LD_LIBRARY_PATH.
that let trac-all -prep run to completion.
cheers,
satra
On Wed, Feb 5, 2014 at 9:02 PM, Satrajit Ghosh sa...@mit.edu
hi all,
we are looking for feedback on learning/using/installing Nipype - any
challenge or hurdle that may have derailed you, wasted your time, left you
wanting a photon torpedo, etc.,.
we are in the process of re-architecting components of Nipype and feedback
would help a lot.
please
of which, is there a patch (a 5.3.1) in the horizon which will
include the tracula updates and perhaps netcdf in the freesurfer download.
cheers,
satra
On Wed, Feb 5, 2014 at 11:07 PM, Satrajit Ghosh sa...@mit.edu wrote:
update: the lack of libnetcdf eventually makes it fail.
i found
hi,
some of our freesurfer directories have become bloated with all kinds of
non-freesurfer data. if i want to rerun a subject in a new location while
maintaining the edits, is there a minimal list of files i should copy over?
cheers,
satra
___
and are subjective, i'd like to provide those as part of data sharing).
cheers,
satra
On Wed, Apr 16, 2014 at 5:16 PM, Satrajit Ghosh sa...@mit.edu wrote:
hi,
some of our freesurfer directories have become bloated with all kinds of
non-freesurfer data. if i want to rerun a subject in a new location
hi a.y.,
is there any part of tracula that currently benefits from openmp or mkl
availability?
cheers,
satra
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The information in
. if myelin
maps were important to your study you might go with T2w (like HCP), but if
lesion detection were more important you might go with FLAIR (like
biobank).
Peace,
Matt.
From: Satrajit Ghosh sa...@mit.edu
Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date
thanks matt.
cheers,
satra
On Wed, Jul 30, 2014 at 2:58 PM, Matt Glasser m...@ma-tea.com wrote:
Yes we performed both on the same subject in the same session and then
compared the myelin map results.
Peace,
Matt.
From: Satrajit Ghosh sa...@mit.edu
Reply-To: Freesurfer support list
...@nmr.mgh.harvard.edu
wrote:
please don't count on the T2 and FLAIR options doing the same thing as I
suspect that they won't in the near future!
Bruce
On Wed, 30 Jul 2014, Satrajit Ghosh wrote:
thanks matt,
would like to be sure that your comments in relation to the T2-space-flair
sequence
looks like the freesurfer wiki is down.
cheers,
satra
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hi bruce,
is there a way to divide consistently (same number of regions and one to
one correspondence - obviously not the exact same areas) across subjects
within aparc regions?
cheers,
satra
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,
satra
On Wed, Oct 3, 2012 at 7:13 PM, John Griffiths
j.davidgriffi...@gmail.comwrote:
Would the Lausanne2008 template from the connectome mapping toolkit not do
the trick?
http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advanced.html
On 3 October 2012 23:18, Satrajit
: aparc.annot - e.g i want to break up stg into 6 regions
subj2: break up stg also into 6 regions such that there is a one to one
correspondence between the subj2 regions and subj1 regions.
cheers,
satra
Bruce
On Wed, 3 Oct 2012, Satrajit Ghosh wrote:
hi john,
thanks. that's the idea, but what i
-sfg+pc
The SFG divisions will have the following names: superiorfrontal,
superiorfrontal_div2, superiorfrontal_div3, superiorfrontal_div4. The
PC divisions will be precentral, precentral_div2, precentral_div3.
On Sat, 6 Oct 2012, Satrajit Ghosh wrote:
hi bruce,
I'm not positive I
hi doug,
just to follow up on this. if i had the phase encode direction (we
currently store various dicom attributes in a nifti header extension),
where would i provide it?
cheers,
satra
On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Hi Clark, the phase
hi
matt: could you generate the myelin maps say from two flash scans at
different flip angles?
bruce: if one had a choice between an mprage + t2 flair and 2 flash scans
at 5/20 flip angles, what would be your recommendation?
cheers,
satra
On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser
hi folks,
happy new year.
we are trying to create an object model for the freesurfer directory.
is there a function/script in freesurfer that would return me effectively
something `ls -lR` but only the items that are mandatory for a subjects'
directory?
if not, is there a document that lists
. Maybe just run
recon-all and then ls -lR :)
doug
On 01/05/2013 02:48 PM, Satrajit Ghosh wrote:
hi folks,
happy new year.
we are trying to create an object model for the freesurfer directory.
is there a function/script in freesurfer that would return me
effectively something `ls
hi bruce and others,
are there any specific implications we should be worried about (e.g., with
qdec or surf2surf) when using an fsaverage that's from a different version
that ran the recon.
cheers,
satra
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in spherical
registration, or potentially elsewhere. I don't anticipate any large
changes, but I wouldn't count on them being identical
Bruce
On Mon, 4 Feb 2013, Satrajit Ghosh wrote:
hi bruce and others,
are there any specific implications we should be worried about (e.g.,
with qdec or surf2surf
hi,
if you have pointers to publicly available DICOM data or willing to share
such data publicly from different scanners and acquisition sequences for
structural, diffusion and functional data from human participants, please
contact me off list.
currently, the more varied the scanners and
hi all,
i'm trying to rerun some subjects processed with 5.0 with 5.1 and am getting
the following error on all the subjects.
simply executing recon-all -s subjid -all
any ideas?
cheers,
satra
-- unfolding failed - restoring original position
0750: dt=0.001250,
update: node on cluster had failing memory chip!
cheers,
satra
On Mon, Jul 18, 2011 at 4:16 PM, Satrajit Ghosh sa...@mit.edu wrote:
hi all,
i'm trying to rerun some subjects processed with 5.0 with 5.1 and am
getting the following error on all the subjects.
simply executing recon-all -s
hi mike,
In theory it could, as we use Nibabel for i/o and they support Gifti.
However, I have no data in Gifti format at the moment to work with, so
at the moment I would say we are Freesurfer specific.
freesurfer does support giftis.
mris_convert --combinesurfs fsaverage/surf/lh.inflated
hi all,
when a .img extension file is passed to freesurfer routines, it is read in
as analyze even if the header says it's a nifti image. we have observed that
this causes a left-right flip in some cases. since a .img cannot exist
without a header to be meaningful, shouldn't the appropriate type
hi,
we are seeing a strange freeview issue at mit and just wanted to check if
anybody else has seen this. we are running natty narwhal (ubuntu 11.04).
details here:
https://github.com/gablab/mindhive/issues/1
cheers,
satra
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the freeview from 5.1.0 to your 5.0.0
installation? you would need to copy:
freesurfer/lib/qt
freesurfer/bin/freeview
freesurfer/bin/freeview.bin
freesurver/bin/qt_setup.csh
n.
On Tue, 2011-09-27 at 20:40 -0400, Satrajit Ghosh wrote:
hi,
we are seeing a strange freeview issue at mit
hi folks,
do you happen to have any tool/script that produces a graph of aparc region
neighborhood? with perhaps the edge weight being the length of shared
boundary.
cheers,
satra
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hi pedro,
will this work with gpu instances as well?
cheers,
satra
2011/11/9 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
Some weeks ago I was asked about a public image (AMI) to run in the Amazon
EC2 infrastructure
If you want to use FreeSurfer in the EC2 infrastructure
hi nolan,
i think starcluster is a great way to create a cluster on aws. but for
those wanting to create a single instance and install things on an ami
without actually having a large ami, fabric might be a good option.
fabric:
http://docs.fabfile.org/en/1.3.2/index.html
example: (another
hi nick,
i really like pedro's idea of tracking through instance tracking as opposed
to licenses. on a separate project we are setting up the ability to pull up
as many instances as necessary and install whatever software environment
that's needed to run your analysis. we'll try to ensure that
hi all,
this command: mris_convert --combinesurfs lh.pial rh.pial pial.gii.gz
resulted in lh.pial.gii.gz (the help says it should generate pial.gii.gz).
a related question. once i have this gifti file how do i get
annotations+curvature info also into the file? (the gifti schema supports
this
hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom mwas...@stanford.eduwrote:
Hi Doug,
Is it possible to use the bbregister parameters to resample a functional
image such that it
in the functional space. It would be better to
register
each TR to the anat, then simply sample each TR to the anatomical
space
(volume or surface) rather than going back into functional space.
doug
Satrajit Ghosh wrote:
hey mike,
take a look at:
ftp
by
bbregister, is there any way to use those transformation parameters to take
the function scans into a common space that retains the original voxel size?
Michael
On Mon, Dec 19, 2011 at 1:34 PM, Satrajit Ghosh sa...@mit.edu wrote:
hi michael,
so for each frame of every session you get a bbreg file
depending on what you are doing you could use PySurfer.
cheers,
satra
On Mon, Mar 12, 2012 at 6:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
no, sorry
On Mon, 12 Mar 2012, zhang mingxia wrote:
Hi dear freesurfer experts,
I am making pictures for publication. The images saving
epidewarp.fsl does not take non-integer smoothing kernel sizes.
cheers,
satra
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/brain.nii.gz
Standard error:
if: Badly formed number.
Return code: 1
Interface EPIDeWarp failed to run.
---
On Mon, Mar 26, 2012 at 10:39 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
what does it do? What is the terminal output?
Satrajit Ghosh wrote:
epidewarp.fsl does not take non-integer
hi Qingyang,
you can simply copy and paste the command line into the shell.
cheers,
satra
On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Can you run it outside of the pipeline to assure that it is not a
pipeline issue?
doug
On 03/18/2012 08:54 AM,
howdy brain imagers,
we are trying to put together a vocabulary of DICOM terms and their
definitions related to brain imaging. unfortunately, a lot of the useful
info is often in private tags and these differ from sequence to sequence
and from scanner to scanner.
to help us get at these tags,
hi doug,
we are trying to figure out if for annot we *have to* use sval-annot or if
there is a way to do it with sval?
cheers,
satra
On Fri, May 25, 2012 at 9:46 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
If the source is an annot, then you need to use --sval-annot Is this
causing
such as converting the annot into a
segmentation (mris_annotation2label), passing that to surf2surf with
--sval (and --mapmethod nnf), then converting the output back to an
annotation (mris_seg2annot). This is what happens internally.
doug
On 05/25/2012 09:52 AM, Satrajit Ghosh wrote:
hi doug
if one wants to get at the brain only (similar to bet), is brainmask.mgz the
best file to use? on some of our data, we are noticing a lot of eyeball.
i presume one can use aseg as an alternative. is this more recommended than
brainmask.mgz? also, is the total brain volume computation based on
hi,
mri_convert TrioTim/123456-10-1.dcm test.nii.gz
will scan all files in the dicom directory to get at series 10. in the above
scenario, i know that the files corresponding to the run are
123456-10-*.dcm. is there a way to leverage this information, so that it
does not scan the entire
it seems we could run lh/rh processing stages of recon-all in parallel.
however, i think they will write to the same log files. is there a way to
specify a different log-file prefix?
are there any other common files that these hemisphere based operations
write to? concurrent reading i'm assuming
Hi,
Here is the output of lh.euler.orig for a particular subject:
euler # = v-e+f = 2g-2: 149150 - 447444 + 298297 = 3 -- 0 holes
F =2V-4: 298297 != 298300-4 (-1)
2E=3F:894888 != 894891 (-3)
total defect index = 4
Is there a way of determining which parts of
Is there a cluster/parallel version of freesurfer available?
Thanks,
Satra
--
Satrajit S. Ghosh
Postdoctoral Associate
Speech Communication Group
Research Laboratory of Electronics, MIT
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I see the following statement printed several times through the recon-all
processing and when I try to manipulate images in scuba. Is this something I
can safely ignore?
INFO: Volume /tmp/mritotal_5799/nu_8_dxyz.mnc cannot be found.
Thanks,
Satra
___
Hi,
I'm trying to create an annotation file from a volume is mris_sample_parc.
Is there any way to have it resample at 0.5 the distance between the white
and pial surfaces?
Thanks
Satra
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Is there an easy way to generate a brain mask like aseg.mgz but with the
cortical parcellation included?
Thanks,
Satra
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I'm noticing some discrepancies between the 64 bit and the 32 bit version of
mris_ca_label. I've shown the output from the 64 bit version and the 32 bit
version operating on the same subject. I'm using are the dev versions for
centos from the download site.
To note:
1. In the 64 bit version I get
Dear freesurfer users,
By adding the following phrase to google's search box, you can search the
freesurfer mailing list archives.
site:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
I have found this extremely useful.
Satra
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Hi Bruce and Lars,
Could this be done as a volume atlas and be segmented out by the subcortical
segmentation? That may deal with the lack of high resolution images
necessary for cerebellar parcellation. And I'm not completely sure, but Lars
probably has his data as a volume segmentation if he
for the cerebellum already? I
understand that most T1 images don't have the resolution to do fine surface
structure for the cerebellum, but here I'm looking for rough volume
parcellation based on the major fissures.
Thanks,
Satra
--
Satrajit Ghosh, PhD
Speech Communication Group
Research Laboratory
Hi Bruce,
I'm finding that sometimes the cortical autoparcellation has disjoint areas
with the same label and finger like projections that don't appear
anatomically accurate.
1. Is there any way I can enforce continuity of labels so that I don't get
these islands?
2. Is there any way to enforce
Dear Bruce,
Does the autoseg information get used for surface extraction? For example,
when autoseg classfies the ventricles and basalganglia, are the surface
extraction routines supposed to treat these voxels as part of white matter
and continue? Ideally at the end of the day any place where the
Hi Doug,
I'm using the matlab routine 'read_surf' from the 3.0.3 distribution to read
a surface generated by mri_tessellate.
The magic number for the surface is: 16777213, which does not match either
the QUAD or the TRI magic numbers listed in read_surf and hence does not
read it.
Is there an
Ghosh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] read_surf
Hi Satra,
I think the magic # should still be 16777215. Did your surface get corrupted
somehow?
Bruce
On Thu, 13 Jul 2006, Satrajit Ghosh wrote:
Hi Doug,
I'm using the matlab routine 'read_surf' from the 3.0.3
Hi Joe,
You may want to try realvnc (www.realvnc.com). We have been trying their
enterprise edition and it works really well. The typical vnc server that's
installed does not support OpenGL. I do know that more recent editions of
realvnc do support the GLX extension.
Cheers,
Satra
A further clarification. This has to do with the server end of things, not
the viewer end.
Satra
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Satrajit Ghosh
Sent: Monday, July 17, 2006 1:36 PM
To: 'Joe Berens'; freesurfer@nmr.mgh.harvard.edu
Subject
Is there any documentation for the OASIS freesurfer-processed data? I'm
looking for details of human intervention. For example,
- were seeds inserted for any brains?
- was the white matter edited
- were cortical labels manually edited for correctness?
Any documentation about the whole process
I have 4 files:
F1. anatomical image 1
F2. anatomical image 2
F3. T-map coregistered with anat img 2
F4. xfm file that coregisters anat img 2 to anat img 1.
If I load all of these in scuba and apply the xfm inside scuba to the
data from F2 and F3, everything aligns up nicely with the data from
-06-10 at 15:48 -0400, Satrajit Ghosh wrote:
Hi Nick,
I hadn't heard of freeview. Is there a place we can download it?
Cheers,
Satra
On Wed, Jun 10, 2009 at 3:34 PM, Nick Schmansky
ni...@nmr.mgh.harvard.edu wrote:
Will Freeview work for you? Support for scuba has ended
Hi,
If I have created a direct registration from subj1 to subj2 using
'mris_register -1', is there a way to use mri_surf2surf to transfer labels
from subj1 to subj2 using this registration, i.e., without using a
registration that goes to a common reference?
Alternatively, is there an easy way to
This question was asked on the FSL list and I thought it would be pertinent
on this list as well in relation to mri_convert.
-- Forwarded message --
From: Saad Jbabdi s...@fmrib.ox.ac.uk
The bvecs are supposed to be relative to the image grid.
On 22 Sep 2009, at 13:34, Laura
hi andrew,
i haven't done many systematic comparisons but there are a few practical
considerations to take into account. in recon-all, i believe a few steps
are affected by the openmp option and that creates resource
underutilization. processors run idle when those steps are not being run.
in my
hi jens,
if you search the archives, there is a post that lists the minimal set of
files needed for running recon-all.
i used a tool called cde to create it: http://www.pgbovine.net/cde.html
this reduces the archive down to about 650MB comprising binaries and
atlases.
this wouldn't be for
to find some posts about the minimum files required to run
recon-all, but I cannot find anything. Could you please try to find the
post in the archives and provide me the link?
Thank you very much!
Gesendet: Mittwoch, 19. November 2014 um 15:23 Uhr
Von: Satrajit Ghosh sa...@mit.edu
hi bruce,
we are missing a T1 scan from a participant. is there any pathway in
freesurfer to reconstruct from the T2-flair/flash scan?
cheers,
satra
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probably reject this by default, which you can get around be
> reslicing one of them to be like the other. Or "conforming" both of them.
>
> cheers
> Bruce
> On
> Tue, 31 May 2016, Satrajit Ghosh wrote:
>
> > hi folks,
> > does recon-all work if the input T1s for
hi folks,
does recon-all work if the input T1s for the same participant have
different resolutions? (i don't have a dataset to test, but trying to debug
some issues another group has been having).
cheers,
satra
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