Not sure, cortical thickness maybe?
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 11:57 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] please help me
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thank Bruce
I read several articles and got a little confused.
Can you help me a little if you have any information?
On Saturday, October 24, 2020, 6:04:07 PM GMT+3:30, Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Saman
That’s really a scientific question and up to you!
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 7:17 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me
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hi
Which output can I use to predict age after recon-all?
On Friday, October 23, 2020, 11:46:09 PM GMT+3:30, saman fouladi
<smnfoul...@yahoo.com<mailto:smnfoul...@yahoo.com>> wrote:
yes and replacing -sdir with -sd
thank you very much
On Friday, October 23, 2020, 5:58:11 PM GMT+3:30, Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
You need a -s before the “subj1”
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 2:44 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me
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hi
my code is:
recon-all -i /home/MRI/Training/99060003/T1-image/39501.dcm subj1 -sdir
/home/MRI4 -all
ERROR: Flag subj1 unrecognized.
-i /home/nbml-challenge/Training/99060003/T1-image/39501.dcm subj1 -sdir
/home/team33/MRI4 -all
what is <subject ID you create>??
On Thursday, October 22, 2020, 5:40:05 PM GMT+3:30, saman fouladi
<smnfoul...@yahoo.com<mailto:smnfoul...@yahoo.com>> wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Nifty is a format that a lot of people use (including us) but it is not needed
for our processing. Pick *one* file in your dicom series and pass it to
recon-all:
recon-all -i <path to 1 dicom file> -s <subject ID you create> -sdir <path to
the dir that will contain all outputs> -all
cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me
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hi
Thank you for your response
I have 60 subject MRI that each contains 174 dcm file. and i want predict age
of these subjects. in step one i want extract morphology features and in step2
create a deep learning model that predict age.
According to what I said, what should I do?
If I have to use recon-all with what code can I do this? And what is the use of
nifty?
On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Saman
Recon-all will give you a comprehensive assessment of most macroscopically
visible structures in the brain. You don’t have to convert to nifty first –
just point recon-all at a single slice in the proper dicom series (for your 3D
T1-weighted scan), and it will spend a few hours doing stuff
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] please help me
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hi
I want to process MRI images to extract Morphology features.
I convert my dcm file to nii format by mri-convert command and then I used FSL
software and BET(Best extraction Tool).
Next I do not know what to do to extract morphological features?
My other question is what is the difference between recon-all and use FEAT( in
FSL software)? What are the uses of each?
Thank you
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