Dear Freesurfer community experts,
We're looking to segment the internal capsule using T1 data. We found
documentation in the FreeSurfer white matter segmentation atlas that states
that the right and left anterior and posterior portions of the internal capsule
are segmented as regions 155-158,
I don't think you need to worry about that. We move/copy subject folders
all the time without incident or problem.
On 5/20/19 3:49 PM, Mingzhu Hou wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer team / community,
>
> This is a very basic and general question. I am currently
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Dear Freesurfer team / community,
This is a very basic and general question. I am currently setting up for a
team in our lab to use the Freesurfer automated pipeline for thickness /
volumetric measures on hundreds of adult brains. As there will be
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Hello Caspar,
So are you saying that if you run directly from the terminal in bash (or maybe
in csh with % sign as prompt)
$mri_convert -i inputvolume.mgz--out_orientation LPS-iis .5
-ijs .5 -iks .5-vs 1.2 1.2 1.2
- that the command works, but it
And what about the mask? Display the mask in freeview at a threshold of 0.5
On 5/20/19 3:09 PM, Barletta, Valeria wrote:
>
> This is what I see if I set min 1 max 49 on the overlay
> (the subjectspace.mgh file in the command)
>
>
>
>
>
When you look at the overlay in freeview and set the min thresh to 1, do
you see blobs?
On 5/20/19 2:51 PM, Barletta, Valeria wrote:
>
> I want to extract clusters within the cortical lesion mask in which
> the vertex values are below 49.95
>
> The values are in the file
You will not need to run the entire stream again. Did you run it in
high-res mode? If the volumes are conformed (eg, orig.mgz is 1mm,
252^3), then you do not need to do anything. Otherwise, you will need to
re-run only part of it using the patch and running
recon-all -s subject -segstats
I want to extract clusters within the cortical lesion mask in which the vertex
values are below 49.95
The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh
Thanks,
Vale
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas
Can you send the terminal output?
On 5/20/19 8:51 AM, Michal Tanzer wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
> I am having some difficulties in creating annot file for specific ROIs
> using the 2009atlas. When I am using this command, it saves the annot
> but
How did you choose thresholds of 1 and 49.95? In general, you don't need
to set --thmax. If you input is a binary mask, then you should set
--thmin to somethiing below 1 (eg, 0.5)
On 5/20/19 2:40 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to obtain clusters of vertices
Dear Freesurfers,
I am trying to obtain clusters of vertices whit a certain value over a
threshold inside a lesion mask projected to the surface, with the command:
mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in
lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask
Got it.
Thank you very much for your reply
Mona
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Monday, May 20, 2019 12:52:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mkanalysis-sess refeventdur
They should be there. Can you send recon-all.log and conf2hires.log files?
On 5/20/19 9:59 AM, Bruce Fischl wrote:
> Hi Victor
>
> the lh.white.{KH} are generated from the lh.white file, so I don't
> think it can have skipped creating it. Was it deleted? Can you double
> check?
>
> Bruce
> On
Your attachment says that none of the commands could be found. Make sure
you set up your environment correctly
On 5/20/19 4:53 AM, mustafa amin wrote:
>
> External Email - Use Caution
>
> Hi Bruce,
>
> Thank you for your swift response as always, may I know how to convert
> the more
No, you'll need to change your paradigm file to have two distinct 8 sec
events rather than one 16 sec event.
On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesurfer experts
>
>
> I am making an analysis in Freesurfer version 6 and I have a question
> about the "refeventdur" in
Hi Freesurfer experts
I am making an analysis in Freesurfer version 6 and I have a question about the
"refeventdur" in mkanalysis-sess command.
My stimulus duration is 16 seconds, but for a specific analysis, I only want to
include half of the stimulus duration (ex: the first 8 seconds only
sure. All the fsaverages are in the same space (they are subsets of
fsaverage)
On Mon, 20 May 2019, Loïc Daumail wrote:
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Hi Bruce,
Thanks for your response. Is it also fine for fsaverage5 surface or I need to
switch my data to
fsaverage?
Thanks,
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Hi Bruce,
Thanks for your response. Is it also fine for fsaverage5 surface or I need
to switch my data to fsaverage?
Thanks,
Sincerely,
Loïc
Le lun. 20 mai 2019 à 15:52, Bruce Fischl a
écrit :
> Hi Loic
>
> if you are on the fsaverage surface
Hi Victor
the lh.white.{KH} are generated from the lh.white file, so I don't think
it can have skipped creating it. Was it deleted? Can you double check?
Bruce
On
Mon, 20 May 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
Hi all,
I am running 7T scans through FS6, and I have been
Hi Mustafa
I believe I did:
mri_convert -it dicom IMAGE001 mprage.mgz
recon-all -i mprage.mgz -sd -s -all
you can give it any *single* image in the correct series (don't give it
more than one)
cheers
Bruce
On Mon, 20 May 2019, mustafa amin wrote:
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Hi Loic
if you are on the fsaverage surface you can save the -log10(p) values
using save_mgh.m, then load them in freeview and threshold them or
whatever
cheers
Bruce
On Mon, 20 May 2019, Loïc Daumail wrote:
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Also, one more thing:
My data is
Hi all,
I am running 7T scans through FS6, and I have been recommended to install the
tools in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/
. So I ran the new recon-all.v6.hires, specifically with the command
"recon-all.hires.v6 -s subj -conf2hires -all"
For the
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Dear Freesurfer experts,
I am having some difficulties in creating annot file for specific ROIs
using the 2009atlas. When I am using this command, it saves the annot but I
am getting empty files. Using the same command with the aparc.annot file
and
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Dear all,
We are looking for a post-doc student for our lab at Karolinska institute
in Stockholm. We are doing structural and functional MRI research on
dementia. In current project we are acquiring multimodal MRI on
frontotemporal dementia patients.
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Hi!
Unfortunately, it turns out that downgrading glibc does not solve this
issue, neither with .14 nor with .15 versions.
Doug, we are calling mri_convert from a csh script, with the following
options:
mri_convert -i inputvolume.mgz \
-o
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Hi Bruce,
Thank you for your swift response as always, may I know how to convert the more
than 100 DICOM files to mgz or nifti? I noticed that the command is for 1
file/image, please correct me if I am wrong. The MP-RAGE file that I sent you
is
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Dear Freesurfer experts,
I have a question about the bug in FreeSurfer v.6 in the global metrics
computation:
I have run my data through the longitudinal pipeline. I would like to
know if my analysis have been affected (3T, voxel size 0.94) and I
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Also, one more thing:
My data is on fsaverage5 resolution.
Thanks in advance,
Sincerely,
Loïc
Le lun. 20 mai 2019 à 09:49, Loïc Daumail a écrit :
> Dear Freesurfer community,
>
> I obtained score matrices of surfaces after performing diffusion
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Dear Freesurfer community,
I obtained score matrices of surfaces after performing diffusion embedding
map on fMRI data.
I am now using the SurfStat toolbox(Matlab) in order to obtain p-value maps
to compare between two groups.
After obtaining the
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