Q8FV7PEIuiLy1z3HVp3gbjCsii3j4j03rTzmmPs5FUP-VmkbKWIa7_dLCtbBDJidWYD2UEyV7ab5r6eKb0byoeD5Qd53y4Iok2NVwnUXajXd4ZCe1R8wQt8Ndoe2_mSWLSLu8ae6eDQHoXaJeC_iT1Z1F4-j4b4v9uBN0Fdvvw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>
>>>
>>> It suggests using mri_coreg.
>>>
>>&
gh.harvard.edu%2Ffswiki%2FPetSurferIt
suggests using
mri_coreg.-PaulFrom: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Mahdi Babaei <mahdibabai...@gmail.com>Sent: Sunday,
November 5, 2023 2:25 PMTo: freesur...@nmr.mgh.harvard.eduSubject:
[Fr
4ZCe1R8wQt8Ndoe2_mSWLSLu8ae6eDQHoXaJeC_iT1Z1F4-j4b4v9uBN0Fdvvw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>
>>
>> It suggests using mri_coreg.
>>
>> -Paul
>>
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu <
>>
nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Question about Freesurfer
External Email - Use Caution
Dear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New Jersey,
USA, where my research focuses on MRI to PET tra
harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mahdi Babaei <
> mahdibabai...@gmail.com>
> Sent: Sunday, November 5, 2023 2:25 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Question about Freesurfer
>
> External Ema
tSurfer
It suggests using mri_coreg.
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Mahdi Babaei
Sent: Sunday, November 5, 2023 2:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question about Freesurfer
External
External Email - Use Caution
Dear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New
Jersey, USA, where my research focuses on MRI to PET translation. I have a
number of problems. Freeview opens fine but when I load a column in it just
shows a b
FS does not warp any images. No smoothing is ever applied.
On 11/7/2022 3:30 PM, Katrina Simon wrote:
External Email - Use Caution
Hi, I have a dataset i have run with the default settings of
Freesurfer 6.0. A reviewer for a paper recently raised the question
"Were T1 images warped w
External Email - Use Caution
Hi, I have a dataset i have run with the default settings of Freesurfer
6.0. A reviewer for a paper recently raised the question "Were T1 images
warped with the grey matter preserved? Were volumetric images for the
amygdala and hippocampus smoothed?"
I
I don't know about using R. In FreeSurfer you can run asegstats2table
(for aseg.stats) or aparcstats2table (for aparc.stats). Run with -h to
get help or look at our tutorials
On 9/2/2021 7:26 AM, hyeyoung park wrote:
External Email - Use Caution
Hi,
This is hyeyoung Park from Seoul N
External Email - Use Caution
Hi,
This is hyeyoung Park from Seoul National University in South Korea.
I have one question about FREESURFER.
I ran recon-all using terminal, and finally I got files such as aseg.stats
and aparc.stats.
For the next steps, I'd like to extract the measu
Hi Dorsa
as I said, if you rerun don't include the -i. And please include the full
command and output pasted into the email
thanks
Bruce
On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:
Hi,
Thanks for the help. I ran the following code and I got errors. I have
attached the log.
recon-all
Hi Dorsa
can you just copy and paste the text into the email? It's much easier
than trying to look at images of text.
Your recon-all command finished successfully. Essentially you didn't tell
it to do anything except import the data and create the subject dir.
Typically you want to give the
Hi Dorsa
you need to give us more information that that if you want us to help you.
Send us the full command line you ran and the full screen output and log
files for starters.
cheers
Bruce
On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:
Thank you! When I recon-all my files, I get the foll
Thank you! When I recon-all my files, I get the following error:
files are not found to be different and cannot be sorted
Do you have any suggestions?
Thank you
Dorsa
On Tue, Jun 28, 2016 at 12:57 PM, Bruce Fischl
wrote:
> just give recon-all a single slice from the series with -i name>. I
just give recon-all a single slice from the series with -i . It will figure out
the rest of them
On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:
> Hi,
> I am a little confused about how should I save my files to execute recon-all
> on
> them. I have 240 slices of dicom format and I put them in
Hi,
I am a little confused about how should I save my files to execute
recon-all on them. I have 240 slices of dicom format and I put them in a
folder in my subjects_dir. but I get errors when using recon-all on the
folder containing the MRIs. Can you help me with that? I really appreciate
your he
Hi,
I need patient specific brain models created by warping atlases to
individual MRIs. I want the model to include the Subthalamic Nucleus, Gpi,
Thalamus and their surrounding organs. (Cortical segmentation is not
necessary). When I use the" recon all "command on one MRI image, I get the
error "c
Hi Dorsa
what specific models do you need? The 10-20 hours is to process the data
from a single subject at a single timepoint. If you check out our wiki
(http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and
sample datasets and such
cheers
Bruce
On Mon, 27 Jun 2016, Dorsa
Hi,
I am graduate student at the University of Michigan and I am performing
research on deep brain stimulation. I want to warp an anatomical brain
atlas to individual patient MRIs to get the patient specific brain models
out of it. I chose FreeSurfer to do this and I have installed it on my
comput
Hi,
I've been trying to understand the FScoordinates powerpoint and I would like to
ask a few questions (these questions might simply be about mri_convert,
depending on where my confusion is...).
1) I think the orig.mgz volume is in the CRS space. Now, looking at slide 8 in
the powerpoint, if I
Hi Kourosh,
you can ask the freesurfer list for these kind of questions. I believe that
the ras coordinates are not changed, so reslicing everyhting as the original
inputs will be sufficient (no transform, only based on the header
information)
e.g.
mri_convert -rt nearest -rl youroriginialinput
I don't know why they would care, but we can't say for sure
On Wed, 16 Jul
2008, Pedro Paulo de Magalhães Oliveira Junior wrote:
Hi,
Some time ago I have asked a question similar to this and the answer was a
page with a template:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitat
Hi,
Some time ago I have asked a question similar to this and the answer was a
page with a template:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation
I would like to ask two questions:
1) Is this template a copy paste one?
2) Is there any concern regarding plagiarism using thi
24 matches
Mail list logo
