I have used Tksurfer to make image from cross subject statistics maps in
mgh files. Is it possible to use a script to make image with both
hemisphere in lateral and medial view. I would also like to display p
values as 10^-log(p). Is this possible? Can I use Matlat or FDR? How can
I produce
Hi Knut
you can use a tcl script in tksurfer if you want. You are probably
better off doing the 10^-log(p) on your own and saving it as a separate
overlay. There are plenty of tcl scripts in the distribution as examples. A
simple one would be:
set val
FYI
-- Forwarded message --
Date: Tue, 7 Feb 2012 09:15:37 -0500
From: Ziad Saad sa...@mail.nih.gov
To: Bruce Fischl fis...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Conversion of an mgh file to nii
I just realized my post got rejected from the message list since I I am not
Hi - It's hard to tell without access to the actual data, but it sounds
like you've found the right way to reconcile your nifti volume and
gradient directions, so you should pass those to trac-all directly instead
of the dicom.
Anastasia.
On Tue, 7 Feb 2012, Xiangzhen Kong wrote:
Hi
Dear Freesurfer experts,
I have a question regarding mris_divide_parcellation. I have created a file
containing the parcels from aparc.annot that I want to split and I have run
the following command. Why is Freesurfer allocating 36 additional units?
When I open the new annotation file
Hi Yolanda
does the resulting parcellation look ok? I think that's a small bug that
may not have any effect on you (there will just be extra, unused color
table entries)
Bruce
On Tue, 7 Feb 2012, Yolanda Vives wrote:
Dear Freesurfer experts,
I have a question regarding
Hi Experts,
Is there a way to add the CA-4/DG subfield to the output generated by
kvlQuantifyHippocampalSubfieldSegmentations.sh?
Running the command for an individual subject outputs this subfield, but I
wanted to make sure there wasn't an easier route before I start manually
entering each
The Freesurfer group will be offering a three-day Freesurfer Tutorial and
Workshop, April 2-4 at the Martinos Center in Charlestown, MA.
A description of the course, the tentative schedule, and the link to the
registration website can be found here:
Hi Rob,
It seems the internal 5.1 version of FreeSurfer you're running was
somehow compiled on 12 April 2011 (?), whereas the official release
date was 24 May 2011.
Could you please double-check if this is indeed the case? If it is,
could you please run the official release instead? We changed a
Hi Oliver,
You're right: internally we're upsampling the images to 0.5mm
isotropic resolution, so if you had acquired 0.5mm isotropic images
from the start, that would actually be much better (provided you don't
simply trade off SNR for increased image matrix size). The catch with
this is that
Hi Rob,
I think this might be related to the same 5.1 version mismatch I
indicated in my previous email to you. Could you please try if things
start working when you use the official FS release?
Thanks,
Koen
On Mon, Feb 6, 2012 at 1:59 PM, Rob Tennyson te...@nmr.mgh.harvard.edu wrote:
Hi
Hi Rob,
Same reply - the current scripts should do this automatically for you...
Please let me know if you run into trouble with this,
Koen
On Tue, Feb 7, 2012 at 11:18 AM, Rob Tennyson te...@nmr.mgh.harvard.edu wrote:
Hi Experts,
Is there a way to add the CA-4/DG subfield to the output
you could create each of the individual maps, but not the placement and
not the tet
On Tue, 7 Feb 2012, Knut J Bjuland wrote:
Hi Bruce
Is it possible to use ascript to create a similar figure to the jpg file I am
attaching?
Knut J
On 07. feb. 2012 15:09, Bruce Fischl wrote:
Hi Knut
Hi Knut, you can check out my script called tksnap (uses accopanying
mytks.tcl). It will take pics in different orientations. Note: this is
not a supported script, so it's up to you to figure out what it does and
how it does it. I provide it as a way to help you figure this stuff out.
If you
Hi all,
My lab is just starting to use Freesurfer, and are finding that a lot of
our recon-all jobs are needing a fair amount of editing. We've run into a
problem that we can't figure out how to address - on several of our brains,
a large chunk (up to 2/3 of the brain) is missing from the wm.mgz
Hi Nicole
do you want to upload an example subject directory tarred and gzipped? We
almost never see this, so it sounds like something is wrong.
cheers
Bruce
On Tue, 7 Feb
2012, Nicole Senecal wrote:
Hi all,
My lab is just starting to use Freesurfer, and are finding that a lot of our
Hi Heidi, the first contrast is correct assuming that BP is your 2nd
variable. For the second design, you would make use [0 0 1 -1 0 0].
Note that you can do all of these from a single FSGD file (but using
separate ones is ok too).
doug
Jacobs H (NP) wrote:
Dear FreeSurfers,
I have been
Dear Everyone,
First of all, I have been very impressed by the functionality and abilities
of FreeSurfer. I have a question about the longitudinal processing stream.
I have two sets of MRI at two different time points for elderly
individuals. Before version 5.1 came out, I ran the first years
Hi Mark,
So the first thing is you absolutely need to re-run you 1st year data with 5.1
The reason is that you will introduce potential bias by running the different
time points with different software (consistently).
As a side note: The same is basically true when they do software updates on
Hi,
On the off chance that you are comfortable with Python, you may find that
PySurfer http://pysurfer.github.com/ provides a more pleasant scripting
environment than the tcl-based TkSurfer interface :)
Best,
Michael
On Tue, Feb 7, 2012 at 12:46 PM, Douglas N Greve
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