The area.pial file.
Best,
Feng
发件人:Sandy Schramm
发送时间:2015-11-06 15:24
主题:[Freesurfer] extract pial surface
收件人:"freesurfer"
抄送:
Dear experts,
how can I extract pial surface (in mm2) of all our participants?
Performing aparcstats2table -meas area extracts white area.
Thanks,
Sandy
_
Dear experts,
how can I extract pial surface (in mm2) of all our participants?
Performing aparcstats2table -meas area extracts white area.
Thanks,
Sandy
___
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make sure there are no blank lines
On 11/5/15 6:29 PM, Erik Lindberg wrote:
OK, however I tried several options. With the matrix 1 1 1 1 -1 -1 -1
-1 0(using the doss option for age) I basically get the same results
Reshaping mriglm->mask...
search space = 74612.446501
MatrixReadTxT: could
On 11/04/2015 05:10 AM, Erik Lindberg wrote:
>
> Dear Freesurfer experts,
>
> I know this has been an ongoing topic in the mailing list – however I
> would like to raise the issue one more time. In the choice between
> doss and dods – I usually check if there is a significant interaction
> and
The contents of the AAA.mtx matrix are
{1 1 1 1 -1 -1 -1 -1}/4 0
It has to be a simple matrix with simple numbers, no characters, no math
symbols. It will not do the math for you.
On 11/05/2015 05:12 PM, Erik Lindberg wrote:
> Dear Doug,
> attached is the folder I tried to run with the matrix.
How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 256^3, 1mm3 ?
On 11/05/2015 04:47 PM, std...@virgilio.it wrote:
> Please see the file attached.
> Thanks
>
> Stefanofile
>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 5-nov-2015 15.43
> A:
>
white
On 11/05/2015 04:18 PM, Yang, Daniel wrote:
> Dear FreeSurfer Experts,
>
> When I perform aparcstats2table —meas area, does it get it pial.area
> or white area?
>
> I believe it is the pial.area, but this is not documented. If yes,
> what can I obtain white area via aparcstats2table?
>
> T
Please see the file attached.Thanks
Stefanofile
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 5-nov-2015 15.43
A:
Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-FAST
sorry, should have been
fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config
Dear FreeSurfer Experts,
When I perform aparcstats2table —meas area, does it get it pial.area or white
area?
I believe it is the pial.area, but this is not documented. If yes, what can I
obtain white area via aparcstats2table?
Thanks,
Daniel
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mai
1. We don't have much experience with this. 3mm is pretty thick so it may
not work, but the only way to find out is to try
2. I'll leave this for Eugenio.
3. Yes, I think it could help, although note that part of the point of
using T1/T2 is that the bias field cancels
cheers
Bruce
On Thu, 5
Hi Anastasia:
I processed 42 brains on Tracula and it ran without problems. I am now
trying to run them individually on DTK to test another hypothesis. [I am
using the DTK for the first time]. I loaded the diffusion weighted image,
filled the parameters in the GUI and ran one single brain. However
Forwarded Message
Subject:REMINDER: OHBM 2016 Call For Council Nominations Deadline Nov. 9
Date: Thu, 05 Nov 2015 11:36:37 -0600
From: i...@humanbrainmapping.org
Reply-To: i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu
Dear OHBM Member:
Your
Hello Freesurfer experts,
I am working with a database of pre-collected scans. Although the T1
images are collected at 1x1x1 mm^3 resolution, the T2 and proton density
scans are .938x.938x3 mm^3.
1) I wanted to see if you think that using the T2 scans for recon-all would
hurt or help the pial
There is no separate label for Wernike's (it is a functional, not
anatomical, definition). Heschl's gyrus is separate from STG.
Perhaps Christophe can weigh in on his labels.
On 11/5/15 11:42 AM, Ahtam, Banu wrote:
Dear All,
I am new to freesurfer and would appreciate your help with the
fo
Hi Stephanie, can you send me one of your dicoms?
doug
On 11/5/15 11:27 AM, McMains, Stephanie wrote:
We are finding a conversion problem with our latest multiband/SMS data
(Using a sequence from Minnesota). The values can be very large,
greater than 53,000. These large voxels get turned int
Dear All,
I am new to freesurfer and would appreciate your help with the following
questions.
I tried to look through the previous posts but couldn’t find the answers to all
my questions.
Thank you in advance.
Best,
Banu
My question:
I wanted to look at certain language related regions in
We are finding a conversion problem with our latest multiband/SMS data (Using a
sequence from Minnesota). The values can be very large, greater than 53,000.
These large voxels get turned into very large negative numbers when converting
to nii. This happens even if we use the flag –odt float a
Damien Fair's Neuroimaging Lab is looking for a candidate with expertise in
neuroimaging, particularly in the field of MRI. While the main focus of this
position is in neuroimaging, candidates with experience in bioinformatics and
software development are highly encouraged to apply.
The positio
sorry, should have been
fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee doug.log
On 11/4/15 6:05 PM, std...@virgilio.it wrote:
Hi Dough,
in summary:
I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri
thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the
can you send the matrix?
On 11/5/15 5:29 AM, Erik Lindberg wrote:
Dear Freesufer experts,
I have trouble loading a contrast matrix - however I am not sure if
something is going wrong earlier ... and this is causing this problem.
Below is the error messages that I get plus the contrast matrix
On 11/5/15 8:37 AM, John Anderson wrote:
Thanks a lot Doug!
Kindly ...
1. What do you mean by intensity normalized?
Removing non-biological intensity fluctuations such as
darkening/brightening from multiple head coils
2. What is the purpose of conforming the inputs to 256^3 1mm3
This is some
Thanks a lot Doug!
Kindly ...
1. What do you mean by intensity normalized?
2. What is the purpose of conforming the inputs to 256^3 1mm3
3. In order to move mask to diffusion space (FA map) or PET space I do the following:
3.1 I register FA map to T1 ( after converting the DICOMs to
are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from
*different* series or from the *same* series? If they are in the same
series than that explains what is happening. You should only give recon-all
a single file f
Dear Freesufer experts,
I have trouble loading a contrast matrix - however I am not sure if
something is going wrong earlier ... and this is causing this problem.
Below is the error messages that I get plus the contrast matrix and the
.fsgd file I am trying to run.
I checked this previous mesage
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