I'm sure it was registered to the T1w with BBR, though I don't know the
internals of that in recon-all. Given that you might only be the second
person to try this with non T2-SPACE T2w images (and I unfortunately had not
told Bruce about my bad experience with this), you can forgive the
FreeSurfer
Hmm, Ok. Thanks Matt.
I still think it's weird that the T2 didn't seem to ever get registered to
the FS volume, but it's not a huge loss if we can't use them. With that
said, it might help to clarify the docs on this point a bit, as it sort of
sounded like any reasonably-sized T2-weighted image wo
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So the T2-SPACE is a variable flip angle sequence that actually has a fair
amount of T1 and MT contrast in it and relatively less T2 contrast. As a
result, you can clearly see the difference between grey and white matter,
and CSF is not massively brighter than grey and white matter. If you are
us
Hi Matt,
It's this sequence:
http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)
You can click the console screenshots for a closer view of the parameters
-- let me know if you need me to track down more info.
mw
On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser wrote:
> Som
It is more or less mni305. I would use mri_vol2vol but I think that
mri_convert should give you the same result.
doug
On 09/27/2013 03:02 PM, Paul Beach wrote:
> -- Forwarded message --
> From: *Paul Beach* mailto:pabea...@gmail.com>>
> Date: Fri, Sep 27, 2013 at 2:39 PM
> Subj
-- Forwarded message --
From: Paul Beach
Date: Fri, Sep 27, 2013 at 2:39 PM
Subject: Re: [Freesurfer] Question about talairach.m3z file
To: Bruce Fischl
So would you suggest, then, that it would be better to use the mri_vol2vol
command to transform subject data (anatomical and f
Someone sent me a different kind of T2w image and it didn't work so well,
so we need to know what kind of image this is.
Peace,
Matt.
On 9/27/13 1:33 PM, "Bruce Fischl" wrote:
>nope, pretty much only with T2-space with and without a flair pulse
>On Fri,
>27 Sep 2013, Matt Glasser wrote:
>
>>
nope, pretty much only with T2-space with and without a flair pulse
On Fri,
27 Sep 2013, Matt Glasser wrote:
> Also, what kind of T2w sequence is this? I think we've mostly tested it
> with the T2-SPACE (unless Bruce has tested with other things).
>
> Peace,
>
> Matt.
>
> On 9/27/13 12:58 PM, "B
Also, what kind of T2w sequence is this? I think we've mostly tested it
with the T2-SPACE (unless Bruce has tested with other things).
Peace,
Matt.
On 9/27/13 12:58 PM, "Bruce Fischl" wrote:
>Hi Michael
>
>that looks pretty bad! What is the resolution of the T2? The T1 that you
>overlay on al
Hi Michael
that looks pretty bad! What is the resolution of the T2? The T1 that you
overlay on also looks somewhat blurry - what was it?
Bruce
On Fri, 27 Sep
2013, Michael Waskom wrote:
Hi, just to make the problem a bit more transparent, I took a second
screenshot of the slices with the
Hi, just to make the problem a bit more transparent, I took a second
screenshot of the slices with the pial surface from the -T2pial run in red
and the pial surface from the normal run in cyan:
https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
On Fri, Sep 27, 2013 at 10:37 AM, Mich
Hi,
I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the
pial mesh.
However, I've found that using the T2 is causing rather dramatic problems
with the pial surface.
I processed the same subject's data with and without the -T2pial option.
Here are links to a) pial surface imag
Hi Freesurfers,
I just looked at my cortical thickness results, in which I performed an
interaction between group (2 groups) and cognition (continuous).
I see regions popping up, which is great! Especially since they are related to
the task.
Now, I made a scatterplot of some of these vertices to
Hi Lucia - The bvecs file is full of "0,000". I'm guessing the problem
is that your environment is set to use the comma instead of the point as
the decimal separator. Can you try this and then rerun?
setenv LANG en_US.UTF-8
Hope this helps,
a.y
On Fri, 27 Sep 2013, Lucia Billeci w
Anastasia thank you very much!
I have wrote to FSL mail list.
They have uploaded a new web page of FDT.
Anyway, these are the commands:
mris_convert lh.white lh.white.giiecho lh.BA44.label lh.BA45.label >
listOfAreas.txt
label2surf -s lh.white.gii -o lh.BA44.gii -l listOfAreas.txtStefano
---
Hi Anastasia
here are the files
Thanks
Lucia
bvals
Description: Binary data
bvecs
Description: Binary data
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Dr. Lucia Billeci, PhD
Institute of Clinical Physiology (IFC)
National Research Council (CNR)
via Moruzzi 1, 56124, Pisa
ITALY
Tel: +39-
Thanks Zeke,
I'll run the subjects again,
Gari
On Fri, Sep 27, 2013 at 4:48 PM, Z K wrote:
> Yes, there will be some minor differences between centos4 and centos6
> build. The differences are due to the different versions of gcc used for
> the different distributions. The centos6 build uses a n
Hi Lucia - The nb0 thing isn't used any more, it was in the old version of
tracula only (the one in freesurfer 5.1).
Can you send the version of the bvecs and bvals files that are in the
dmri/ directory?
Thanks,
a.y
On Fri, 27 Sep 2013, Lucia Billeci wrote:
> Dear Anastasia,
>
> I added in t
You may have to give up the arcuate (slft) too, since part of the temporal
lobes are chopped off. Although it didn't get to that tract so it's just a
guess.
Yes, you should be fine by removing from pathlist (and the respective
entries in ncpts) any tracts that are partly cut off in your imag
Yes, there will be some minor differences between centos4 and centos6
build. The differences are due to the different versions of gcc used for
the different distributions. The centos6 build uses a newer version of
gcc which has optimization options not available on the version gcc for
the cento
label2surf is an FSL command, so you can get a more authoritative answer
on the FSL list, but I'd try one of the files in the surf/ directory, like
lh.white or rh.white.
On Fri, 27 Sep 2013, std...@virgilio.it wrote:
Hi list and Anastasia.
Thank you very much. mri_annotatiion2label works f
Many thanks Anastasia.
So, do you think it would work if I exclude this tracts from the analysis
and ask for the remaining ones?
thanks again,
Gari
On Fri, Sep 27, 2013 at 4:35 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Gari - Just looked at your subject. The bottom of
Hi Gari - Just looked at your subject. The bottom of the brain is
truncated in the DWIs. The slices stop in the middle of the angular
bundle, which is why the -prior step failed in that pathway. But I expect
there'd be problems with other tracts that reach that inferior, even if
they didn't f
Dear Anastasia,
I added in the dmrirc file the following line:
set nb0 = 1
because I red in the forum that it is necessary to indicate the number of b0
volume and I don't get the error about fslroi anymore. However now I have the
following error:
Error: bvecs and bvals don't have the same n
Great, thanks Bruce!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 27, 2013 9:36 AM
To: pfot...@nmr.mgh.harvard.edu
Cc: freesurfer@nmr.mg
Hi Paul
not really. It is a nonlinear transform to our own atlas, which is
loosely in MNI space. Doug can probably give you a more precise answer
cheers
Bruce
On
Fri, 27 Sep 2013, Paul Beach wrote:
Hello Freesurfer community,
I have a question about the file talairach.m3z, which is found i
Hi Panos
yes, mri_convert will do this with -odt int
cheers
Bruce
On Fri, 27 Sep 2013,
pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> I was wondering whether there is a way to convert a FLOAT type niftii file
> to an INT type niftii file.
> Thanks in advance!
>
> Best,
> Panos
>
I see, thanks Doug!
> It is --sum, not --sumfile
> doug
>
>
> On 09/25/2013 12:44 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS Community,
>>
>> I am using the mri_volcluster command but for some reason the --sumfile
>> shows up as an unknown flag. Is there another way to get a summary text
>> f
Hello Freesurfer community,
I have a question about the file talairach.m3z, which is found in the
mri/transforms directory of all subjects that have undergone recon-all. I
am utilizing this file in an mri_convert script to resample AFNI processed
T1volumes (and time-series data) to MNI space. Howe
Hi FS Community,
I was wondering whether there is a way to convert a FLOAT type niftii file
to an INT type niftii file.
Thanks in advance!
Best,
Panos
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/li
Hi Joy-Loi
read_curv.m should do the trick.
cheers
Bruce
On Fri, 27 Sep 2013, Joy-Loi Chepkoech
wrote:
> Dear FreeSurfer experts,
>
> I am looking for a way to read a subject's cortical thickness and
> volume, and surface area at each vertex into a vector that is readable
> by matlab.
> How s
Hi Doug,
it would be great if you could give me some further advise on the group
analysis of functional connectivity maps.
Specifically, I am trying to get PCC maps for certain seeds, and am not
planning any comparison between groups.
Following your previous advise, I am running isxconcat-sess with
*Dear Freesurfers,*
I apologize if this question has already been asked somewhere - I didn't
manage to find the answer in the archives.
I have my T1 images processed in FS_5.3 and corresponding PET images
co-registered with rawavg.nii-images in SPM (converted from mgz). Now I
would like to extract
Thanks Doug!
Because it maps from a MNI152 space to the FreeSurfer average space, do you
know what register.dat I can use?
Is it some sort of inverse mni152.register.dat?
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
How to detect group differences between groups with low group size like
for instant n=8 vs n=50?
Are there any statistics measures I could use like looking at
interaction between group and gender, or should I use doss? Is it
feasible to design a custom based design matrix?
Knut J
Hi list and Anastasia.
Thank you very much. mri_annotatiion2label works fine.
Becouse I should run this command:
label2surf -s -o -l
-s,--surf input surface-o,--outoutput surface
-l,--labels ascii list of label files
I should provide also surface file re
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