What exactly is the problem? You only specified the lh.inflated, so it
is not unusual that that is the only thing you see. If it is that you
were expecting some activation (colors) on the surface, then try
reducing the threshold (4 is pretty high)
On 12/06/2016 05:41 PM, Shady Rahayel wrote:
>
Hi,
I was conducting GLM analysis using the command line. Everything seemed to
work fine until I wanted to visualize the uncorrected significance map
using the following command (my glmdir folder for the contrast is
lh.scheme1.glmdir):
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=ap
On 12/06/2016 04:57 PM, Xavier Guell Paradis wrote:
>
> Dear FS team,
>
> We are designing an fMRI experiment that has to include one motor, one
> cognitive and one affective task. We would like to use a rapid
> event-related design because we want to do MVPA to classify patients
> vs controls
That is a little easier. In matlab you can
seg = MRIread('youseg.mgz');
out = seg;
out.vol = zeros(size(out.vol));
ind = find(seg.vol == segno);
out.vol(ind) = valueforsegno;
MRIwrite(out,'out.mgz');
On 12/06/2016 05:04 PM, Hao wen wrote:
>
>
> Hello, I checked your script, I think this is
Hello, I checked your script, I think this is to map the aparc.annot, I have
already done that, what I want is to map the aseg.annot subcortical
segmentation like what we can do for aparc, so do you have any idea??
Thanks in advance
De : Hao wen
Envoyé : mardi 6
Dear FS team,
We are designing an fMRI experiment that has to include one motor, one
cognitive and one affective task. We would like to use a rapid event-related
design because we want to do MVPA to classify patients vs controls. We have 4
questions regarding Optseq:
1) We are designing a task
Hi,
I have DWI data from two subjects acquired using b-values of 0 for the B0's
and 700 for the DWI's. There are 10 B0's and 60 DWI's in each dataset. I
was successfully able to follow the instructions to use TRACULA on data
from a single subject (recon-all; then trac-all -prep, -bedp, and -path),
Not sure. This one did not look like a mosaic (it had 256x256 voxels).
Can you run it without anonymization?
On 12/06/2016 01:40 PM, Marianna Riello wrote:
> Yeah they do not come directly from the scanner. They are anonymized.
> The same were the enhanced version of the dicom (with 170 files pe
It may be that the registration is off. You should load your gm volume
with the surfaces on top, something like
tkmeditfv -f orig.mgz -aux gm_values2anat.nii -surfs
On 12/06/2016 01:41 PM, Ilaria Mazzonetto wrote:
>
> Hi Freesurfer User,
>
> I would like to map a volume to a surface. I have a
Hi Freesurfer User,
I would like to map a volume to a surface. I have a T1 image (SubjX) with
resolution 1x1x1 and a gray matter mask with resolution 6x6x6. The voxels
in the lower resolution image (gm_values.nii) have zero value if they are
not in the gray matter and a value between 0.1 and 20 if
Yeah they do not come directly from the scanner. They are anonymized.
The same were the enhanced version of the dicom (with 170 files per dicom) but
these in particular didn't show any error with mri_convert.
So why should these mosaic ones show the error?
Thanks,
Marianna
-Original Mess
This file is missing critical information. Did this come directly from
your scanner or was it changed in some way (eg, anonymized)?
On 12/06/2016 10:32 AM, Marianna Riello wrote:
> Yes I did it, I used your mail but it gives me an error.
> Check attachment.
>
> -Original Message-
> From:
Thanks very much, I will try to look at that:)
Perfect FS,hahah
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Douglas Greve
Envoyé : mardi 6 décembre 2016 17:51
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] Volumetric Group Analysis:
correct, my email address
On 12/6/16 11:08 AM, dgw wrote:
> Marianna,
>
> I think Doug means:
>
> gr...@nmr.mgh.harvard.edu
>
> hth
> d
>
> On Tue, Dec 6, 2016 at 10:32 AM, Marianna Riello wrote:
>> Yes I did it, I used your mail but it gives me an error.
>> Check attachment.
>>
>> -Original
This is a tricky thing to do. I've created a matlab file to help, which
you can get from here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
Look at the help for an example on how to use it. You will have to
specify the list of ROI names and the corresponding list o
Marianna,
I think Doug means:
gr...@nmr.mgh.harvard.edu
hth
d
On Tue, Dec 6, 2016 at 10:32 AM, Marianna Riello wrote:
> Yes I did it, I used your mail but it gives me an error.
> Check attachment.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurf
Yes I did it, I used your mail but it gives me an error.
Check attachment.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Tuesday, December 6, 2016 10:23 AM
To: freesurfer@nmr.mgh.harvard.e
I did not. You should have had an opportunity to enter an email address
of the recipient. You can use my email
On 12/5/16 6:35 PM, Marianna Riello wrote:
> I uploaded the dicom mosaic on Martinos Center.
> I am wondering whether you received it
>
> -Original Message-
> From: freesurf
Hello, FS experts:
I have a question for visualizing statistical analysis asegstats2tbale result
into a map like what we have done in qdec, which uses the thickness
information, so if i want to use the volume information of the different
segmentation volume, and after doing z-score for two grou
Dear all,
We've run longitudinal Freesurfer on 30 healthy subjects. We have two
subgroups (n=15) and we found a significant longitudinal change in the left
and right cerebellar cortex in one of our subgroups. However, this change
is very small: mean=0.67% range: -1.61-2.3% for the right cerebellar
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