Bruce, thanks a lot. I will look forward for Jonathan's reply.
On 31/10/2012 13:11, "Bruce Fischl" wrote:
>Hi Lena
>
>sorry, I havne't heard of Phase-Sensitive Inversion Recovery. I'll cc Jon
>Polimeni who might have some thoughts.
>
>cheers
>Bruce
with PSIR sequences. Any suggestions/thoughts will
be helpful.
Cheers,
Lena Palaniyappan
This message and any attachment are intended solely for the addressee and may
contain confidential information. If you have received this message in error,
please send it back to me, and immediately
ion, did you by any
> > chance download the snow leopard executables?
> >
> > a.y
> >
> > On Sat, 1 Oct 2011, Lena Palaniyappan wrote:
> >
> > > Dear Anastasia & Team
> > >
> > > I am running trac-all on 5.1 but my recons were
but the script
exits when priors are being drawn.
Can you help please? I downloaded the most stable version last week. (could it
still be the library dependency eror?)
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Wellcome Trainin
HI Doug
Do we now have the means for computing point to point asymmetry differences
between RH and LH? I remember you mentioned we may have something on this line
with 5.1
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Well
Hi all
is it possible to obtain the surface area computations for each of the
parcellations in Destrieux annot from pial instead of white surfaces? As the
vertex addresses are likely to be different between white and pial surfaces, I
suppose the following command is not appropriate - any ideas
Hi Lisa
Are you able to see the paths traced from the 'intermediate' files - you can
find them in a tmp folder within the subject's surf directory
Lena
On 04/04/2011 16:24, "Lisa Ronan" wrote:
Dear List
I have recently come up agains the same problem as described below, namely the
error w
t the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
___
Lena Palaniyappan
Hi all
I have a ROI label on left hemisphere - I need to map this ROI onto right
hemisphere to get a homologous region (for testing hemispheric differences).
What is the best way for doing this?
Cheers
Lena
--
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychi
/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychia
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message and any attachment are intended solely for the addressee and may
contain confidential i
On 26/12/2010 12:08, "Lena Palaniyappan"
wrote:
For some of my data, label2label (one of the PALS labels from fsaverage being
mapped on to a subject) gives this message
Performing mapping from target back to the source label
ERROR: srcvtxno = -1 < 0
trgvtxno = 140122, dmin = 1
es/FREECOM/Applications/freesurfer/subjects/conn/fsaverage/label/lh.aparc.label
Any help?
Thanks
Lena
____
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centr
f/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!
Darwin pmc10113.nottingham.ac.uk 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
Is there any workaround/patching?
Cheers
Lena
___
Lena Palaniyappa
get surface could
not be mapped to a vertex in the source surface
because the xyz of the target is outside of the
range of the hash table
Is there anything I can do to circumvent this?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lectu
RS at Sat Dec 25 09:23:23 GMT 2010
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
Th
I have MATLABR2010b, on a Mac 10.6.4, using freesurfer 5.0
I am not able to getmatlab when I invoke freesurfer
Can someone help?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( Universit
etter off just using
mri_label2label to propagate the PALS labels to other subjects.
cheers
Bruce
On Sat, 18
Dec 2010, Lena Palaniyappan wrote:
>
> Is it legit to create a .gcs file using fsaverage as the sole subject for the
> PALS parcellations?
>
> I intend to use this .g
Is it legit to create a .gcs file using fsaverage as the sole subject for the
PALS parcellations?
I intend to use this .gcs to mri_ca_label all my subjects.
Please advise,
Lena
On 18/12/2010 13:57, "Lena Palaniyappan"
wrote:
I want to use the annot file for lobar areas in fsave
e.reg subjid/label/lh.PALS_Lobes.annot
For this purpose.
What cortical classifier file should I use to map the different PALS atlases
(at least - the two of them : Brodmann and Lobes)
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Hon
words, I
want to generate a single image on an average surface, that shows the regional
differences between the correlated thickness maps. Is this feasible?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychi
ACC parcellated when PCS is absent,
Hope someone can help
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham |
I want to compare vertexwise differences in thickness between R and L
hemisphere in two groups is there any workaround to create a statistical
asymmetry map for this purpose?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary
registration
> matrix, which will depend on where the volume came from.
>
> doug
>
> Lena Palaniyappan wrote:
>> I have a mask file which I need to overlay on the individual images of
>> a group of subjects to extract thickness values within ht mask. But
>>
I have a mask file which I need to overlay on the individual images of a
group of subjects to extract thickness values within ht mask. But the mask
is of dimension 2X2X2, will this be an issue?
Thanks
Lena
___
Lena Palaniyappan
Clinical
. Do you need seed coordinates in the
> native DTI space of each subject or in MNI space? If MNI, which one, mni152 or
> mni305? Do you need the coordinates in xyz or row,col,slice? Or do you need
> your seed region to be a mask (in what space)?
>
> doug
>
> On 8/12/10 8:55 AM, L
should be registered to the average structural MPRAGE
of the group
How do I then go on to obtain the coordinates for my label on the DTI space?
Many thanks
Lena
>
>
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of
: make_average_surface
+++
Any help will be much appreciated,
Thanks
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottin
Is there any way I can recon-all for images that have cerebellum missing?
These fail repeatedly at talairach, no-talcheck flag doesn¹t help
Cheers
thanks
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychi
Hi all,
How do I replace talairach.xfm by an identity matrix to prevent reorienting
of images when I make-average ?
Cheers
Lena
This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system:
you are advised to
he___defaultstructureksup/&RH=1200651
> 159612>
>
> Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
> 37032 Tours - France
> tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.ed
not included cerebellum fully in the slices: is this a problem?)
>> Thanks for your help
>>
>> On 08/07/2010 16:05, "Bruce Fischl" wrote:
>>
>>> well that certainly looks wrong. What does the original image look like?
>>> On
>>> Thu,
ena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment
opefully lh.sulc will do the job.
>
> On 06/18/2010 08:49 AM, Lena Palaniyappan wrote:
>> Hi all
>>
>> I am trying to determine a 'sulcal pit' - the deepest point in central
>> sulcus. The lh.curv file gives curv values of all vertices, but how can I
>>
Hi all
I am trying to determine a 'sulcal pit' - the deepest point in central
sulcus. The lh.curv file gives curv values of all vertices, but how can I
display the depth as a color map localised to central sulcus only? With such
a display will I be able to identify the zone with maximum 'depth' a
of the movement vector
> with the surface normal, although at the end the global mean is taken out
> of it. Will that work for you?
>
> cheers
> Bruce
>
>
> On Sun, 13 Jun 2010, Lena Palaniyappan wrote:
>
>> I located some discussions but could noit figure out ho
I located some discussions but could noit figure out how can I obtain
numerical depth values from ?h.sulc files. I need to find the sulcal dept of
certain sulci as defined in aparc.a2009
Thanks in advance
Lena
This message has been checked for viruses but the contents of an attachment
may still c
ent slope) and DOSS (different
> offset same slope) GLM analysis in qdec. Did you take this into account in
> your ROI analysis?
>
> Cheers,
>
> Martin
>
> On Sun, May 23, 2010 at 7:09 PM, Lena Palaniyappan
> wrote:
>> While doing an age corrected qdec compariso
values and looked at the means, I could not see the same direction of effect
why could this be? Is this a problem with smoothing (I used FWHM 20 for
looking at whole brain comparisons)
Cheers
Lena
___
Lena Palaniyappan
PhD student & Honorary
?
Cheers
Lena
___
Lena Palaniyappan
PhD Student & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the
I don't seem to get freeview on commandline - where can I download this?
Thanks
LKP
On 19/05/2010 17:47, "Bruce Fischl" wrote:
> Hi Lena,
>
> I'm not sure you can do this in tkmedit. You might try freeview instead.
>
> cheers
> Bruce
> On
&g
I want to show a group of 5 labels ach with a different color in tkmedit
(Orig.mgz) display can I manipulate the colors of these lables I am able
to do this in tksurfer: not tkmedit. Am I missing something?
Cheers
Lena
___
Lena
does freesurfer handle this issue I am using freesurfer to
compute gyrification values: this is a major issue any help will be
appreciated
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( Unive
0.4520.4270.6610.6080.5311.1820.41
0.4760.4810.7770.5590.6770.5470.417
How can I get the parcellation labels displayed?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary
interested in only few of the Destrieux
parcellations: is there any way I can do this?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens
Is there any reference available for tracking the boundaries of 5
parcellations within insula as given by Destrieux a2009s?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottin
advance
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but t
gz -segmentation wmparc.mgz
>
> which uses the default color table.
>
> n.
>
> On Tue, 2010-02-16 at 18:21 +, Lena Palaniyappan wrote:
>> Dear Nick
>>
>> This is exactly what I have been doing for last 3 days!!! - took the last 2
>> commands and made
I managed to obtain outputs from recon-all lGI now I would like to obtain
a mean gyrification index (not sure if the mean is meaningful?!) for all
vertices within 3 ROIs as defined by Destrieux atlas -
How should I do this? Can I treat lGI surfaces just as thockness maps in
which case can I us
\_
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment
may still contain software virus
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment
may still co
I want to use contrast files that are outputs from SPM (in IMG HDR format)
to overlay on inflated surfaces.
But if I use bbregister and choose T1 as the image type, the regisration
achieved is poor (image attached)
Is this the correct way of doing this or am I missing something?
Commands used:
be not projecting contrasts from a differently
registered image set onto reconstructed freesurfer anatomical?
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Bloc
possible?
Will I be better off doing FSL_VBM instead - if that is easy to run with
freesurfer?
cheers
Lena
Lena Palaniyappan
PhD student| Division of Psychiatry ( University of Nottingham)
South Block 'A' floor| Queens Medi
?
___
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the
___
Lena Palaniyappan
Division of Psychiatry ( University of Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could d
Though the pial surface and wm surface follow expected course, there are
some regions that are misclassified when the colortable is overlaid. Please
see the example below... Should I worry?
Thanks in anticipation
LKP
___
Lena Palaniyappan
__
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
___
Lena Palaniyappan
Clinical Lecturer &
o tell left from right
> (it's probably why you have a flip).
>
> We don't have much experience with dicom. Have you tried using -it dicom in
> mri_convert to be explicit about the format?
>
> cheers,
> Bruce
>
>
> On Thu, 30 Jul
> 2009, Lena Palani
--
Hello group
I am new to freesurfer. I have two problems. Please accept my apologies if
these queries are bit naïve!
Any help will be much appreciated. I am trying to autorecon1 a single image
obtained from Philips 3T as dicom output. I use MacOS X11 terminal.
1. I am not able to use mri_c
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