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 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
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
Dear users
We are, fortunately, being increasing asked to provide clinical scanning
slots for the NHS and for Lodestone. This has the desirable effect of
providing income. It has the disadvantage that there is less flexibility
in being able to offer slots for research scanning, especially when the
research is part of a pilot project that is unfunded.
The agreement with Lodestone is that they will attempt to use free slots
left after the Thursday noon cut-off for booking by research PIs. Please
book your time for the week ahead by booking before Thursdays at noon.
Lodestone will then take the remaining slots for single case work. The
only exception to this is Lodestone NHS work which will continue to
occupy half day slots so that block booking of patients can be used
several weeks ahead of time.
There is little pressure on scanners in the evenings (at the moment). If
you are a trained operator then please consider using evening slots for
your research. If you wish to become trained in operating MRI then
please let us know so that we can start a training course for those
interested. The advantage is that evening scanning is cheaper, at the
moment.
Gary
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
Dear ynic-users
At the Thursday evening sessions this term we have been describing the
changes in YNiC and building up to the first official release of YNiC
software and documentation. We are very pleased to be able to announce
that the release date will be the 8th of January 2008. This is earlier
than we had originally planned and reflects the enormous amount of
effort that everyone has put into getting the software and documents
into a complete package. This could not have been done without the
co-operation of the users who carried out the beta testing. Further
information about the complete contents of the first release will be
circulated next week.
We had initially planned to hold masterclasses this term to go through
current software and applications. But as we can now confidently say
that the new software will be released early in the new year, it makes
sense to hold the masterclasses after that release so that everyone can
take full advantage of all the new features and the more complete help
documentation. Therefore we would like to postpone the masterclasses.
Instead we would like to hold the roundtable discussion on the use of
the eye-tracker. We also have a new user who would like to make a
project presentation.
We would like to suggest that the Thursday sessions now look like this
for the rest of term
Thursday 29th Nov 2007 : Project presentation by Dr. Srimant Tripathy
from Bradford
Thursday 6th December : Roundtable discussion on use of the eye-trackers
Thursday 13th December : Project presentation by Gary Green
Thursday 20th December : Christmas drinks
and then
Thursday 10th January 2008 : The new software and documentation
Thursday 17th Jan : Masterclass on the new visualisation software
Thursday 24th Jan : Masterclass on MEG analysis techniques
Thursday 31st Jan : Masterclass on MRI analysis techniques
We then propose that we start the roundtable discussions about what
should be in the second release
comments welcome
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
November 22nd
1. Update on analysis tools at YNiC
2. MRI
FSL
2.1 Features: Atlases, Bedpostx and FIRST, avw2fsl
2.2 Scripts and batch processing (python demo)
2.2 Higher level analyses (?)
2.3 Cluster Feat and Cluster Other
OTHER (Freesurfer, SPM, mrVista)
3. MEG tools
3.1. Beamforming and permutation statistics
4. Visualisation tools at YNiC
4.1 FSLVIEW
4.2 YNICDV3D
5. Support & Documentation at YNiC
6. Users' requests and what we can do better
All welcome, refreshments will be provided afterwards.
--
Will Woods
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
Hi Laura,
Rapid event-related fMRI has many advantages for cognitive neuroscience
research. However, the main problem with this technique is that the
signal is very small compared to a block design. One way to increase
the signal-to-noise ratio is to increase the number of trials. This
typically means using a short ISI (otherwise your subjects could be in
the scanner for a long time!). It is also good to vary the ISI to avoid
expectation effects (i.e the subject predicting when the next event is
likely to occur). However, the problem with a short ISI is that the
response to one stimulus will likely overlap with the response to the
next. This is not a problem if the BOLD response is linear (i.e. the
response to two successive stimuli is the same as adding the response to
two independent stimuli with an appropriate temporal offset). However,
a number of studies have found that there are significant
non-linearities when the ISI is less than ~5sec (eg Dale and Buckner,
1997; Huetell and McCarthy, 2000). So, varying ISI can have positive
and negative effects on the BOLD signal. I haven't used the programs
that Claire and Silvia are using, but I assume they are trying to find
an optimum balance between these effects.
Users - please feel free to correct or comment!
Tim
Laura Lee wrote:
> Hi MRI-support,
>
> I'm struggling along trying to work out how to create a 'stochastic'
> event-related design for fMRI. Claire Moody has passed on a program
> that searches for the optimum stimulus schedule (she & Silvia used it
> for their last project). I've read over all the bumpf but am still
> quite confused by all the new concepts. I think I know roughly what I
> want but then there are some parameters I am unsure about and don't
> really understand the implications of the settings. I'd be really
> grateful if you could give me a hand.
>
> This is the programme I downloaded...
> http://surfer.nmr.mgh.harvard.edu/optseq
> And there's a pretty comprehensive help page here...
> http://surfer.nmr.mgh.harvard.edu/optseq/optseq2.help.txt
>
> Thanks, Laura
>
>
>
>
>
--
Dr Tim Andrews
Department of Psychology
University of York
York, YO10 5DD
UK
Tel: 44-1904-434356
Fax: 44-1904-433181
http://www-users.york.ac.uk/~ta505/http://www.york.ac.uk/depts/psych/www/admissions/cns/
Dear all,
there is another interesting paper in the 'Articles of interest' section of:
https://www.ynic.york.ac.uk/doc/Miscellaneous
This one is on combined MRI / MEG, which may or may not be of interest you.
If you have any papers to add to this section, forward them to me and
I'll make them globally available.
Thanks,
Michael
--
Dr Michael Simpson
Science Liaison Officer
York Neuroimaging Centre
Innovation Way
York
YO10 5DG
Tel: 01904 567614
Web: http://www.ynic.york.ac.uk
Elena Solesio has been visiting YNiC from the imaging centre in Madrid.
Today, Thursday lunchtime, at 1:00pm, Elena will be giving a talk in
YNiC open plan on some of the work she's been doing, entitled:
Retroactive Interference Modulates Magnetic Brain Activity In Normal
Aging: A Magnetoencephalography Study.
All are welcome to come along.
-----------
At 4pm today, there is a YNiC update seminar
1. update on MEG
2. recap of MEG facilities at YNiC
3. what is new and what has changed
4. sensor space and source space
5. beamforming update
6. minimum norm and dipoles
7. Users' requests and what we can do better
All welcome
Refreshments will be served after the seminar
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
