External Email - Use Caution
Hi Stefano,
We just figured out the issue. But there are a few things I might need to
clarify with you:
1) Yeo2011 original parcellation or Yeo2011 split labels version
May I know which parcellation version you would like to use?
We provide two
External Email - Use Caution
Doug,
I have implemented the new version of the command. I am getting this error when
I add the no-prune flag to my script.
ERROR: could not find volume --no-prune. Does it exist?
ERROR: reading --no-prune
Are there specifics with where in the
FYI
-- Forwarded message --
Date: Thu, 28 Mar 2019 01:53:47 +
From: "Amir Shmuel, Dr."
To: Bruce Fischl
Subject: Symposium on Advances in High-Field MRI in Montreal, right after ISMRM
External Email - Use Caution
Hi Bruce,
I’d appreciate it if you could
External Email - Use Caution
Thank you Bruce I will tell them
Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara
> On 27 Mar 2019, at 20.49, Bruce Fischl wrote:
>
> I see. Then they will have
External Email - Use Caution
Many thanks Bruce
Cheers!
Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara
> On 27 Mar 2019, at 20.48, Bruce Fischl wrote:
>
> no, it does not need contrast
External Email - Use Caution
Thank you very much Matt
Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara
> On 27 Mar 2019, at 18.19, Glasser, Matthew wrote:
>
>External Email - Use
External Email - Use Caution
Hi,
I am interested in the Hippocampal Subfields And Nuclei Of Amygdala module and
have a few questions regarding its functionalities.
Regarding the segmentation of amygdala nuclei, you say that currently, "volumes
of the nuclei must be
External Email - Use Caution
Can you send us snapshots of what you are seeing? I am not sure what you
mean by "labels of different colors that disagree with anatomical location
and boundaries of the networks".
On Thu, Mar 28, 2019 at 12:08 AM wrote:
> My apologies, the right
It looks like the dicom file is the localizer/scout. It is not the
anatomical (eg, only 3 slices). You can try running dcmunpack to get a
list of runs in the dicom folder. Then pass one of the dicoms from the
anatomical to recon-all
On 3/27/19 4:50 PM, Z Hessam wrote:
>
> External
no, not really. You can use multiple --replace optoins, eg, --replace
-117 2 --replace -118 2 ...
On 3/27/19 6:08 PM, Song, Da-Yea wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I have a set of binary mask files that I’m trying to assign different
> values to. Currently I’m
External Email - Use Caution
Hello,
I have a set of binary mask files that I'm trying to assign different values
to. Currently I'm doing:
mri_binarize --i sub001.nii.gz --o final_sub001.nii.gz --replace -117 2
mri_binarize --I sub002.nii.gz --o final_sub002.nii.gz --replace
Great!
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 of
External Email - Use Caution
They are sagital T1 mpr mri.
On Thursday, March 28, 2019, Z Hessam wrote:
> I get them from a mri center
>
> On Thursday, March 28, 2019, Bruce Fischl
wrote:
>> where did you get the dicoms?
>> On Thu, 28 Mar 2019, Z Hessam wrote:
>>
>>>
>>>
External Email - Use Caution
I get them from a mri center
On Thursday, March 28, 2019, Bruce Fischl
wrote:
> where did you get the dicoms?
> On Thu, 28 Mar 2019, Z Hessam wrote:
>
>>
>> External Email - Use Caution
>>
>> Soory , why this error has been occured? How the
where did you get the dicoms?
On Thu, 28 Mar
2019, Z Hessam wrote:
External Email - Use Caution
Soory , why this error has been occured? How the column of all zero is made?
On Tuesday, March 19, 2019, Bruce Fischl wrote:
> p.s. you can see this in the log file:
>
> Image
External Email - Use Caution
dcmdump the dicoms and the info will be in the hdr
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra
Sent: Wednesday, March 27, 2019 4:44:14 PM
To: Freesurfer support list
Subject:
Dear Freesurfer experts
Hi
I am trying to extract the time of data acquisition for each run from the
functional data and compare it with my paradigm files.
I thought the numbers in DICOM file names (ie,
MR.1.3.12.2.1107.5.2.43.67026.2019011316475911712728505 ) are correspondent
with the
External Email - Use Caution
My apologies, the right hemisphere does not contain the color of each region
but only an unique color. The left hemisphere contains labels of different
colors that disagree with anatomical location and boundaries of the networks.
If I use the
External Email - Use Caution
Additional issue: the colortable does not fit with the atlas and with anatomy
of networks.
> Il 27 marzo 2019 alle 16.17 Thomas Yeo ha scritto:
>
>
> External Email - Use Caution
>
>
>
> Hi Stefano,
>
> How are
External Email - Use Caution
Thanks the right hemiphere is ok, but the left no.
> Il 27 marzo 2019 alle 16.17 Thomas Yeo ha scritto:
>
>
> External Email - Use Caution
>
>
>
> Hi Stefano,
>
> How are you using the colortable? Are you just
External Email - Use Caution
Hi Stefano,
How are you using the colortable? Are you just passing it as a flag to
mri_aparc2aseg?
As far as I know (and I am NOT very knowledgeable, so I could be wrong),
the volumetric file (Yeo_17Net.mgz) does not contain the color information.
So
External Email - Use Caution
The problem persists.
We are sure that the command lines which I'm using are corrected?
> Il 27 marzo 2019 alle 16.10 Thomas Yeo ha scritto:
>
> Hi Stefano,
>
> Did you see the colortable that Aihuiping attached? Does it work for you?
>
>
External Email - Use Caution
The problem persists.
We are sure that the command lines which I'm using are corrected?
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot
External Email - Use Caution
Hi Stefano,
Did you see the colortable that Aihuiping attached? Does it work for you?
Thanks,
Thomas
On Wed, Mar 27, 2019 at 11:08 PM wrote:
> Please see the attached file.
>
>
> Il 27 marzo 2019 alle 15.39 Thomas Yeo ha
> scritto:
>
>
External Email - Use Caution
Please see the attached file.
> Il 27 marzo 2019 alle 15.39 Thomas Yeo ha scritto:
>
>
> External Email - Use Caution
>
>
>
> Hi Stefano,
>
> Can you attach your updated colortable, so we can take a look?
>
>
External Email - Use Caution
You dont have to go all the way into a cifti space dlabel you could use the
steps I sent to create a labeled nifti
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Valentina Mancini
Sent: Wednesday,
External Email - Use Caution
Hi Stefano,
Can you attach your updated colortable, so we can take a look?
Thanks,
Thomas
On Wed, Mar 27, 2019 at 10:27 PM wrote:
> Yes the left hemisphere is fine.
>
> The error occurs again. The labels for posterior DMN and anterior DMN
> are
External Email - Use Caution
First of all, I would like to thank you all for your help.
#Eugenio: yes probably there is a way to manually import the thalamic lookup
table in FSLeyes. However, I don't have to use the thalamic segmentation in
FSL, but in SPM and it would be much
External Email - Use Caution
Yes the left hemisphere is fine.
The error occurs again. The labels for posterior DMN and anterior DMN are the
same and numbered like 1016 and 2016, despite I have modified the txt.
Thanks
Stefano
> Il 27 marzo 2019 alle 13.09 Thomas Yeo ha
External Email - Use Caution
wb_command -volume-label-import LR_amyhipthal.nii.gz
$templatedir/SUBCORT_LR.txt LR_amyhipthal_labeled.nii.gz
this is with the amy and hip but can be done with just the thalamus
you just need to edit the label file
External Email - Use Caution
We have run the thalamic and amyhip segmentation scripts on HCP data and were
convert the segmented native nuclei into cifti space including the subcortial
nifti
set thal = ${subjid}_ThalamicNuclei.v10.T1
mri_convert -rt nearest -rl
External Email - Use Caution
Thanks, Valentina.
The thalamic nuclei were included in the FreeSurfer lookup table in the
development version, so I doubt they’d be included in the FreeSurfer HSV. Is it
possible to add them manually?
Also: why don’t you use Freeview to visualize
Usually, an intensive study is done with any new tracer in which they do
arterial sampling and apply various kinetic models to determine which
one fits best (including which regions to use for high binding in
MRTM2). You should find this study for your tracer. For FDG, MRTM2 is
not appropriate
External Email - Use Caution
Hi Eugenio,
Yes, when I move the cursor I can see different pixel values corresponding to
the different areas of the thalamus.
In FSLeyes you can select different lookup tables, and there is one called
"Freeseurfer HSV", but it doesn't work
External Email - Use Caution
Hi Valentina,
I've never used FSLeyes but I suspect you'd need a lookup table to visualize
the nuclei properly. Do you see different pixel values when you move your
cursor over the different areas of the thalamus in FSLeyes?
Cheers,
/Eugenio
--
and your full command line for conversion?
On Wed, 27 Mar 2019, Iglesias
Gonzalez, Eugenio wrote:
External Email - Use Caution
Dear Valentina
Resolution should not be affected by MRI_convert. Can you please send us an
example/screen capture?
Cheers
Eugenio
Sent from
I see. Then they will have mprage sequences and you should be set
On Wed, 27
Mar 2019, mustafa amin wrote:
>External Email - Use Caution
>
> I am going to use Phillips Achieva 1.5 Tesla by the way. Thank you in advance.
>
> Mustafa M. Amin
> Consultant Psychiatrist in Biological
no, it does not need contrast (in fact contrast would make it
more difficult for FreeSurfer to process the data)
cheers
Bruce
On Wed, 27
Mar 2019, mustafa amin wrote:
>External Email - Use Caution
>
> Hi Bruce,
>
> I mentioned and showed the MP-RAGE protocol along with 3D
External Email - Use Caution
Dear Valentina
Resolution should not be affected by MRI_convert. Can you please send us an
example/screen capture?
Cheers
Eugenio
Sent from mobile, please excuse brevity and typos
From: Valentina Mancini
Sent:
External Email - Use Caution
Dear Zheng,
Did the segmentation run to completion?
Can you please send us the output?
Cheers
Eugenio
Sent from mobile, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of 郑凤莲
External Email - Use Caution
Hi Stefano,
Sorry. Can you confirm left hemisphere is ok?
I think in this version of the annot file, the right hemisphere regions
will start off as 2058, rather than 2001. So instead of numbering from 2001
to 2057, it should be from 2058 to 2114.
External Email - Use Caution
No you do not need IV contrast for running FreeSurfer. Rather it would be
better if that was not done.
Matt.
On 3/27/19, 12:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
mustafa amin" wrote:
>External Email - Use Caution
>
>I
External Email - Use Caution
I have renumbered and run:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is
visualized
External Email - Use Caution
Dear all,
I ran the thalamic segmentation implemented in FreeSurfer and, according to
visual inspection, I got nice results with a good delineation of all the nuclei.
Then, I wanted to use the label of the thalamic nuclei to select an ROI in the
External Email - Use Caution
Hi Doug, thanks for the explanation. My question is more related to how we
might go about knowing what are the high binding regions for any tracer? If I
am going to do an FDG-PET study, will the HB region parameters be different
from a
External Email - Use Caution
Hi experts,
I have segmented the thalamic nuclei into 25 nuclei using the new FS version.
However, when I input "freeview -v nu.mgz -v
ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview,
just nu.mgz. What's the matter? Please
46 matches
Mail list logo
