This afternoon's seminar is a new project presentation
"Functional imaging with hyperpolarised carbon dioxide"
4pm, ynic open plan
all welcome
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
York
YO10 5DG
tel (+44) (0) 1904 435349
fax (+44) (0) 1904 435356
mobile 07986778954
On a related note, grad students and post-docs can apply for a $750
travel bursary. It's not much money (especially with the ever-declining
value of the USD) but better than paying the entire £760 airfare yourself!
Deadline is April '08. See link below:
http://ric.uthscsa.edu/hbmtravelawards/
Cindy
Dear YNiC Users
Users are invited to take part in an MRI operator training course held
at YNiC.
Clinical scanning is currently placing a high demand on the MRI
facilities. To provide more flexibility for MRI research scanning,
especially for unfunded projects, we would like to encourage Users to
become MRI operators so that they can collect their own data during
off-peak hours (after 5 pm).
At this point please could you let me know if you, or other members of
your research team, are …
[View More]interested in becoming MRI operators. Once we
have an idea of numbers, we will plan a training schedule that will be
as convenient as possible for everyone involved.
N.B.
1) MRI operators must have a valid first aid certificate. You need to
have a first aid certificate before you are allowed to operate the MRI
scanner independently.
2) Two qualified MRI operators must be present for out-of-hours
scanning. Therefore you will need to train at least two members of your
research team, or co-ordinate your scanning with other qualified MRI
operators.
Best wishes
Rebecca
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
[View Less]
Dear users
Tonight is the first of our roundtable discussions on the future at
ynic. The topic is 'eye-tracking'
Andy Ellis will lead the discussion but contributions/presentations from
others are welcome.
The aim of these roundtables is to discuss what/why/how/when we might
attempt to address a particular need within the user community at YNiC.
All welcome
Refreshments will be available.
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
…
[View More]Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
[View Less]
FYI.
It may be of interest to some of you. They also have a summer session
for this course.
Uzma
Human Brain Anatomy Course
2nd-4th April 2008
Venue: Institute of Child Health
Suitable for undergraduates/postgraduates in neuroscience, medicine and
psychology.
- 3-day programme, assumes minimal prior knowledge
- emphasises functional and clinical neuroanatomy
- includes dissecting-room sessions examining real brains!
_
__http://www.neurocourses.com/_
Dear all,
Today's Psycholinguistics Research Meeting meeting is going to be held
in A202, at 12.30. Our guest is Eytan Zweig, who has recently joined
the linguistics department at York. He
will be discussing MEG work carred out with Liina Pylkkänen at NYU
investigating a visual M170 effect of morphological complexity.
Best,
Shane
Dear list,
The Psycholinguistics Research Group will be hosting a talk by Eytan
Zweig, who has recently joined the linguistics department at York. He
will be discussing MEG work carred out with Liina Pylkkänen at NYU
investigating a visual M170 effect of morphological complexity.
The talk will be held in A202, at 12.30 Monday 3rd, and should last
around an hour.
Shane
Dear list,
I do hope this (general availability of Freesurfer) will happen soon, as the
tool looks very useful indeed, and Pádraig's results shows it achieves good
results without manual intervention.
You can use for a variety of important analyses that are simply not possible
in e.g., FSL, SPM
*Reconstruct the cortical surface and project functional data onto
it - very important in understanding topographical organization of cortical
function (e.g., retinotopy) which is otherwise obscured …
[View More]in the volumetric
data.
*Automatically identify/label cortical regions on the basis of
anatomical landmarks (e.g., fusiform gyrus, motor cortex etc.) Good for
anatomical ROIs
*Automatically identify/label "subcortical" regions (i.e., regions
not on the cortical surface including amygdala, hippocampus, caudate etc.)
Good for anatomical ROIs and volumetry
*Analyse functional group data in a more meaningful space (i.e., one
in which different subjects cortical surfaces are aligned to shared sulcal
landmarks) Good for statistical significance?
*Measure local cortical thickness, curvature etc. Useful for
structural analysis.
I have placed some pictures onto my web page to give an idea of the
segmentation possibilities
http://www-users.york.ac.uk/~th512/cortical_seg_neuroimage.jpghttp://www-users.york.ac.uk/~th512/subcortical_seg_neuron.jpg
Check out their publications for more information:
http://surfer.nmr.mgh.harvard.edu/fswiki/ArticlesSlidesAndPosters
Many thanks to Pádraig for his sterling work in blazing this trail.
Best wishes,
Tom Hartley
(BTW I tried mailing the pictures as attachments, and but the message got
stuck on the server - the mailing list doesn't forward messages over 40KB)
-----Original Message-----
From: Pádraig Kitterick [mailto:p.kitterick@psych.york.ac.uk]
Sent: 29 November 2007 17:34
To: ynic-users(a)ynic.york.ac.uk
Subject: Re: Freesurfer @ YNiC - IMPORTANT UPDATE
Dear list,
Please ignore my previous instructions for installing freesurfer on YNIC
machines. Gary and Mark have just pointed out a very critical point about
doing this: due to the size of the freesurfer package (>3Gb), it is not
feasable to have users installing their own copies of the software as the
disk usage would be considerable. YNIC are looking into ways of provide
freesurfer to all users from a central location sometime in the future.
Apologies for any confusion,
Padraig
Pádraig Kitterick wrote:
> Dear list,
>
> If anyone else is considering using Freesurfer
> (http://surfer.nmr.mgh.harvard.edu/) to reconstruct cortical surface
> models from T1 volumes collected at YNiC, you might be interested in
> the following information.
>
> By default, if you feed a standard structural YNIC T1 into freesurfer
> it will most likely produce spurious brain extractions, and have great
> difficulty (read: 40+ hours of processing!) in reconstructing the
> cortical surfaces. After exploring these problems for a while, I
> discovered two issues which require some pre-processing to solve. The
> first is that freesurfer does not like images with a FOV larger than
> 256mm^3. Standard YNIC T1 structurals have a FOV measuring
> 176x290x290mm
> (176x256x256 slices of 1 x 1.13 x 1.13mm).
>
> In addition to this, the voxel dimensions are misinterpreted by
> freesurfer when it attempts to resample the volume to 1x1x1m voxels,
> which it does as a standard part of the importing process. They are
> interpreted incorrectly as 1.13 x 1.13 x 1mm! Needless to say, this
> leads to all kinds of problems, resulting in spatially distored output
> surfaces.
>
> Therefore, I would recommend that the following steps are taken before
> trying to carry out any processing with freesurfer:
>
> 1) Manually resample the T1 to 1x1x1mm and force the correct
> dimensions to be used, with the 'mri_convert' command (part of the
freesurfer package):
>
> mri_convert -iis 0.9999 -ijs 1.1328 -iks 1.1328 -ois 1 -ojs 1 -oks 1
> -oic 176 -ojc 290 -okc 290 T1.nii.gz T1_1mm.nii.gz
>
> Here, we specify the input sizes (1x1.13x1.13mm), the output sizes
> (1x1x1mm), and I have also specified the number of output slices which
> is important because otherwise mri_convert will truncate them to a
> maximum of 256.
>
> N.B.: This command _should_ be identical for all standard YNIC T1
> structurals. However, it is always important to check that your slice
> counts and sizes are the same as the example given here, otherwise all
> subsequent processing will be compromised.
>
> 2) Remove unnecessary slices from outside the head and the neck so
> that the final number of slices is less than or equal to 256 in all
> dimensions with avwroi (from fsl):
>
> avwroi T1_1mm T1_1mm_reslice x_start x_size y_start y_size z_start
> z_size
>
> where T1_1mm is the resampled MRI (no .nii.gz extension),
> T1_1mm_reslice is the output volume (again, no .nii.gz extension), and
> the _start and _end parameters specify the starting slice and the
> number of slices to include in each dimension (use fslview to find the
> slice numbers). For example, to remove the first and last 17 slices in
> the Y and Z dimensions, we could run:
>
> avwroi T1_1mm T1_1mm_reslice 1 176 18 256 18 256
>
> which would leave us with a FOV of 176x256x256mm, compatible with
> freesurfer. Be careful that only redundant slices are removed!
>
> Your pre-processed volume should now consist of less than or equal to
> 256 slices in each dimension, with 1x1x1mm voxels. This can be safely
> processed with freesurfer using:
>
> recon-all -i T1_1mm_reslice.nii.gz -subjid <subject id> -autorecon-all
>
> Finally, make sure you apply all of this to a copy of the T1, as you
> won't be able to modify the original in the mridata folder, and even
> if you can you really shouldn't!
>
> I hope this will save someone a bit of time and a lot of headaches!
>
> p.s. if you want to install freesurfer in your home folder on YNIC
> machines, follow these steps:
> 1) Download the freesurfer PowerPC distribution and register for a
> licence file on their website: http://surfer.nmr.mgh.harvard.edu/
> 2) Double-click on the image file, and a window will open which
> contains a single package file.
> 3) Right-click on the package file and choose 'Show pacakge contents'
> 4) In the new window that opens, navigate into the 'Contents' folder,
> and drag the Archive.pax.gz to your desktop.
> 5) Double click on the archive file and wait for it to decompress
> (this will take a long time)...
> 6) You should now have a freesurfer folder on your desktop, which you
> can drag into your home folder. Now remove the archive files on your
> desktop as they are quite large and are no longer needed.
> 7) Open a text editor and copy&paste the following:
>
> export FREESURFER_HOME=~/freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> and save the file as 'freesurfer-config' in your home folder. Note
> that this script presumes that you have moved the freesurfer folder
> into your home folder.
> 8) Copy your licence file into your freesurfer folder.
> 9) In an X terminal, type 'source ~/freesurfer-config'. You can now
> use freesurfer commands. Make sure you run this command in X11 each
> time you log in to have access to freesurfer.
>
> Padraig.
>
--
Pádraig Kitterick
Graduate Student
Department of Psychology
University of York
Heslington
York YO10 5DD
UK
Tel: +44 (0) 1904 43 3170
Email: p.kitterick(a)psych.york.ac.uk
--
ynic-users mailing list
ynic-users(a)ynic.york.ac.uk
https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users
[View Less]
Dear list,
If anyone else is considering using Freesurfer
(http://surfer.nmr.mgh.harvard.edu/) to reconstruct cortical surface
models from T1 volumes collected at YNiC, you might be interested in the
following information.
By default, if you feed a standard structural YNIC T1 into freesurfer it
will most likely produce spurious brain extractions, and have great
difficulty (read: 40+ hours of processing!) in reconstructing the
cortical surfaces. After exploring these problems for a while, I
…
[View More]discovered two issues which require some pre-processing to solve. The
first is that freesurfer does not like images with a FOV larger than
256mm^3. Standard YNIC T1 structurals have a FOV measuring 176x290x290mm
(176x256x256 slices of 1 x 1.13 x 1.13mm).
In addition to this, the voxel dimensions are misinterpreted by
freesurfer when it attempts to resample the volume to 1x1x1m voxels,
which it does as a standard part of the importing process. They are
interpreted incorrectly as 1.13 x 1.13 x 1mm! Needless to say, this
leads to all kinds of problems, resulting in spatially distored output
surfaces.
Therefore, I would recommend that the following steps are taken before
trying to carry out any processing with freesurfer:
1) Manually resample the T1 to 1x1x1mm and force the correct dimensions
to be used, with the 'mri_convert' command (part of the freesurfer package):
mri_convert -iis 0.9999 -ijs 1.1328 -iks 1.1328 -ois 1 -ojs 1 -oks 1
-oic 176 -ojc 290 -okc 290 T1.nii.gz T1_1mm.nii.gz
Here, we specify the input sizes (1x1.13x1.13mm), the output sizes
(1x1x1mm), and I have also specified the number of output slices which
is important because otherwise mri_convert will truncate them to a
maximum of 256.
N.B.: This command _should_ be identical for all standard YNIC T1
structurals. However, it is always important to check that your slice
counts and sizes are the same as the example given here, otherwise all
subsequent processing will be compromised.
2) Remove unnecessary slices from outside the head and the neck so that
the final number of slices is less than or equal to 256 in all
dimensions with avwroi (from fsl):
avwroi T1_1mm T1_1mm_reslice x_start x_size y_start y_size z_start z_size
where T1_1mm is the resampled MRI (no .nii.gz extension), T1_1mm_reslice
is the output volume (again, no .nii.gz extension), and the _start and
_end parameters specify the starting slice and the number of slices to
include in each dimension (use fslview to find the slice numbers). For
example, to remove the first and last 17 slices in the Y and Z
dimensions, we could run:
avwroi T1_1mm T1_1mm_reslice 1 176 18 256 18 256
which would leave us with a FOV of 176x256x256mm, compatible with
freesurfer. Be careful that only redundant slices are removed!
Your pre-processed volume should now consist of less than or equal to
256 slices in each dimension, with 1x1x1mm voxels. This can be safely
processed with freesurfer using:
recon-all -i T1_1mm_reslice.nii.gz -subjid <subject id> -autorecon-all
Finally, make sure you apply all of this to a copy of the T1, as you
won't be able to modify the original in the mridata folder, and even if
you can you really shouldn't!
I hope this will save someone a bit of time and a lot of headaches!
p.s. if you want to install freesurfer in your home folder on YNIC
machines, follow these steps:
1) Download the freesurfer PowerPC distribution and register for a
licence file on their website: http://surfer.nmr.mgh.harvard.edu/
2) Double-click on the image file, and a window will open which contains
a single package file.
3) Right-click on the package file and choose 'Show pacakge contents'
4) In the new window that opens, navigate into the 'Contents' folder,
and drag the Archive.pax.gz to your desktop.
5) Double click on the archive file and wait for it to decompress (this
will take a long time)...
6) You should now have a freesurfer folder on your desktop, which you
can drag into your home folder. Now remove the archive files on your
desktop as they are quite large and are no longer needed.
7) Open a text editor and copy&paste the following:
export FREESURFER_HOME=~/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
and save the file as 'freesurfer-config' in your home folder. Note that
this script presumes that you have moved the freesurfer folder into your
home folder.
8) Copy your licence file into your freesurfer folder.
9) In an X terminal, type 'source ~/freesurfer-config'. You can now use
freesurfer commands. Make sure you run this command in X11 each time you
log in to have access to freesurfer.
Padraig.
--
Pádraig Kitterick
Graduate Student
Department of Psychology
University of York
Heslington
York YO10 5DD
UK
Tel: +44 (0) 1904 43 3170
Email: p.kitterick(a)psych.york.ac.uk
[View Less]
