FYI
-- Forwarded message --
Date: Fri, 27 Jul 2018 01:43:03 +
From: "Amir Shmuel, Dr."
To: "Amir Shmuel, Dr."
Subject: Resting-State and Brain Connectivity 2018: Added Events & Submission
Deadline
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Resting State and Brain Co
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Hello,
I tried to create snapshots with tkmedit, but the output snapshot files are
all black. This is the command:
export SUBJECTS_DIR=./
tkmedit blubber norm.mgz
tkmedit shows the image correctly, but when taking a snapshot it is all
black. No error
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Greetings,
I am trying to convert a surface label (e.g., lh.V1_exvivo.thresh.label) into a
volume to use as an ROI mask.
I have played around with the mri_label2vol command, but I can't seem to get it
to work. Here is the command I am using:
mri_la
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Hi there
This might be a very silly question but I actually cannot find the answer
in the email archive:
Assuming I have loaded a label onto fsaverage in Freeview and want to get
the MNI305 coordinate of that labelled vertex, am I simply using the x,y
Hi FS experts,
I reconstructed several 0.75mm structural images using recon-all v6 with
highres flag successfully and everything looks fine. Now, I want to transform
structural images (norm.mgz, 0.75mm3, 320^3) to the common space (MNI305, 1mm3,
255^3 for freesurfer) using mri_vol2vol with mri/
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Dear Dr Greve, I apologies if I was not clear.
I ran voxel-wise analysis between two groups. I thresholded the resultant
statistical map at p<0.05 then I binarized it. This volumetric statistical map
is in MNI152. I would like to move it to fsaverage
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Hi Bruce,
Thank you for your reply. I will try and let you know.
Best,
Khoi
On Thu, Jul 26, 2018 at 4:29 PM, Bruce Fischl
wrote:
> Hi Khoi
>
> I would recommend trying out version 6 and using the bigventricles flag.
> It works pretty well
>
> chee
If the roi.nii does not include your areas of interest, then they will
be masked out. The mask you create with mri_vol2surf may not be very
accurate since it uses volume-based operation.
On 7/26/18 5:19 PM, John Anderson wrote:
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Dear Dr Greve, thank you so
Hi Khoi
I would recommend trying out version 6 and using the bigventricles flag.
It works pretty well
cheers
Bruce
On Thu, 26 Jul 2018, Khoi Mai wrote:
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Hello,
We are trying to run two subjects through recon-all. The kicker is that these
two hav
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Dear Dr Greve, thank you so much. kindly have one additional question and I
appreciate your response.
I would like to move a mask from MNI152 to fsaverage so I can use it as a mask
in flag --mask in the command "mri_glmfit". Does this procedure reduc
Don't use --regheader, use --reg
$FREESURFER_HOME/average/mni152.register.dat
On 7/26/18 4:40 PM, John Anderson wrote:
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Dear Freesurfer experts,
I have mask in MNI152 space. I would like to register this mask to
fsaverage. How can I do this registration. I
Use the mri.2mm aseg.mgz, eg,
mri_binarize --i aseg.mgz --match 7 8 46 47 --dilate 1 --o cblummask.mgz
This will make a mask of cerebellum GM and WM and dilate it by 1 voxel.
On 7/26/18 4:49 PM, Piero Chiacchiaretta wrote:
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Dear FS group,
I would like to re
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Dear FS group,
I would like to restrict mri_glmfit analysis, on FS-FAST outputs, to the
cerebellum.
Thus, I’m using —mask, adding the mask of cerebellum.
To this aim I can obtain it using mri_binarize. Do you agree?
mri_binarize --i ... --match 8 --o L
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Dear Freesurfer experts,
I have mask in MNI152 space. I would like to register this mask to fsaverage.
How can I do this registration. I am thinking of "mri_vol2surf" as follows:
mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o
mask_
I guess it means the surface of the whole brain, including infratentorial
structures.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[dgr...@mgh.harvard.edu]
Sent: Thursday, July 26, 2018 3
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Hi Yeo,
Amazing. That's exactly what I was looking for.
Thanks
Ehsan.
On Sun, Jul 22, 2018 at 9:05 PM, Thomas Yeo wrote:
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>
> Hi Ehsan,
>
> Not sure if any is exactly what you need:
>
> 1) We have divided the
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Dear FreeSurfer Developers,
We are using your longitudinal processing pipeline (version 6.0) for our study
(n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter
was used on the raw images to adjust for hyperintensities in the i
you'll have to be more specific about what "brain surface contour" means.
On 7/26/18 3:46 PM, Barletta, Valeria wrote:
> Dear Freesurfers,
> I need to extract the brain parenchymal fraction to check brain atrophy in my
> patients.
> The BPF is defined as "the ratio of brain parenchymal tissue vol
Dear Freesurfers,
I need to extract the brain parenchymal fraction to check brain atrophy in my
patients.
The BPF is defined as "the ratio of brain parenchymal tissue volume to the
total volume contained within the brain surface contour".
In the text file aseg.stats, I found this info:
# Measur
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Hi Courtney,
I have two general remarks:
1.)
For comparing n groups, the general rule is to have (n-1) binary
indicator variables (and possibly n-1 interaction variables). One group
(a reference group) will be implictly modeled by the intercept (1) an
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Hello,
Can anyone help me with this? I think it got lost in the pool of email.
Best,
Paul
-- Forwarded message --
From: miracle ozzoude
Date: Thu, Jul 5, 2018 at 12:23 PM
Subject: error with mri_ca_register in long
To: Douglas N Greve
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Thanks a lot Dr. Greve, that really helps.
On Thu, Jul 26, 2018 at 10:45 AM, Douglas Greve
wrote:
> They give different results because they are supposed to. It may be that
> the effect you are seeing without regressing out ICV is due to ICV, and
> w
Dear FreeSurfer experts,
I had sent several times this email since the last few months, and never
obtained any reply. Would anyone be able to provide me little bit of insight
please?
I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0.
b1=0, b2=3000 s/mm2 and diff dire
Definitly do not use --rot 180.
I think the registration matrix goes in the other direction, so try
adding --inv to the command line and changing --targ and --mov
On 7/25/18 8:24 PM, Sims, Sara A wrote:
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Hello,
I am trying to put a mask that I made on the
They give different results because they are supposed to. It may be that
the effect you are seeing without regressing out ICV is due to ICV, and
when you control for ICV the effect goes away. It could also be that the
ICV causes the variance to increase. This is why I asked you to check
the rst
If you are using surface area or volume, then you need ICV
On 7/25/18 1:51 PM, Martin Juneja wrote:
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Dr. Greve,
I am sorry if my questions were not clear in previous email.
Basically, I do not know what to conclude from this gamma comparison
i.e. with and
Right!
:)
Thanks
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf
You need to run fcseed-sess to generate that.
> Hi all
>
>
> I am running a seed to whole brain connectivity analysis. I am using the
> labels that I have made from functional ROIs.
>
> When I run fcseed-config, It makes the configuration file but not the .dat
> files.
>
> Here is my command:
>
>
Hi all
I am running a seed to whole brain connectivity analysis. I am using the labels
that I have made from functional ROIs.
When I run fcseed-config, It makes the configuration file but not the .dat
files.
Here is my command:
fcseed-config -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_su
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