External Email - Use Caution
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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution 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
External Email - Use Caution
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 bfischl@mgh.harvard.edu wrote:
#yiv4456525891 #yiv4456525891 -- _filtered {} _filtered {} _filtered {}#yiv4456525891 #yiv4456525891 p.yiv4456525891MsoNormal, #yiv4456525891 li.yiv4456525891MsoNormal, #yiv4456525891 div.yiv4456525891MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv4456525891 span.yiv4456525891ydp1ac82ctlid-translation {}#yiv4456525891 span.yiv4456525891ydpe810003dtlid-translation {}#yiv4456525891 span.yiv4456525891ydpbc4bf220tlid-translation {}#yiv4456525891 span.yiv4456525891ydp44042622tlid-translation {}#yiv4456525891 span.yiv4456525891EmailStyle23 {font-family:sans-serif;color:windowtext;}#yiv4456525891 .yiv4456525891MsoChpDefault {font-size:10.0pt;} _filtered {}#yiv4456525891 div.yiv4456525891WordSection1 {}#yiv4456525891 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
hi
I want to process MRI images to extractMorphology 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] please help me
External Email - Use Caution 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 <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
hi Bruce thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce bfischl@mgh.harvard.edu wrote:
#yiv6786467954 #yiv6786467954 -- _filtered {} _filtered {} _filtered {}#yiv6786467954 #yiv6786467954 p.yiv6786467954MsoNormal, #yiv6786467954 li.yiv6786467954MsoNormal, #yiv6786467954 div.yiv6786467954MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv6786467954 a:link, #yiv6786467954 span.yiv6786467954MsoHyperlink {color:blue;text-decoration:underline;}#yiv6786467954 p.yiv6786467954msonormal, #yiv6786467954 li.yiv6786467954msonormal, #yiv6786467954 div.yiv6786467954msonormal {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv6786467954 span.yiv6786467954ydp1ac82ctlid-translation {}#yiv6786467954 span.yiv6786467954ydpe810003dtlid-translation {}#yiv6786467954 span.yiv6786467954ydpbc4bf220tlid-translation {}#yiv6786467954 span.yiv6786467954ydp44042622tlid-translation {}#yiv6786467954 span.yiv6786467954EmailStyle31 {font-family:sans-serif;color:windowtext;}#yiv6786467954 .yiv6786467954MsoChpDefault {font-size:10.0pt;} _filtered {}#yiv6786467954 div.yiv6786467954WordSection1 {}#yiv6786467954 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Wednesday, October 21, 2020 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
hi
I want to process MRI images to extractMorphology 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 smnfouladi@yahoo.com wrote:
hi Bruce thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce bfischl@mgh.harvard.edu wrote:
#yiv9925090239 -- filtered {}#yiv9925090239 filtered {}#yiv9925090239 filtered {}#yiv9925090239 p.yiv9925090239MsoNormal, #yiv9925090239 li.yiv9925090239MsoNormal, #yiv9925090239 div.yiv9925090239MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv9925090239 a:link, #yiv9925090239 span.yiv9925090239MsoHyperlink {color:blue;text-decoration:underline;}#yiv9925090239 p.yiv9925090239msonormal, #yiv9925090239 li.yiv9925090239msonormal, #yiv9925090239 div.yiv9925090239msonormal {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv9925090239 span.yiv9925090239ydp1ac82ctlid-translation {}#yiv9925090239 span.yiv9925090239ydpe810003dtlid-translation {}#yiv9925090239 span.yiv9925090239ydpbc4bf220tlid-translation {}#yiv9925090239 span.yiv9925090239ydp44042622tlid-translation {}#yiv9925090239 span.yiv9925090239EmailStyle31 {font-family:sans-serif;color:windowtext;}#yiv9925090239 .yiv9925090239MsoChpDefault {font-size:10.0pt;}#yiv9925090239 filtered {}#yiv9925090239 div.yiv9925090239WordSection1 {}#yiv9925090239 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Wednesday, October 21, 2020 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
hi
I want to process MRI images to extractMorphology 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You need a -s before the “subj1”
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] please help me
External Email - Use Caution 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 <smnfouladi@yahoo.commailto:smnfouladi@yahoo.com> wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
yes and replacing -sdir with -sd
thank you very much On Friday, October 23, 2020, 5:58:11 PM GMT+3:30, Fischl, Bruce bfischl@mgh.harvard.edu wrote:
#yiv5801540211 #yiv5801540211 -- _filtered {} _filtered {} _filtered {}#yiv5801540211 #yiv5801540211 p.yiv5801540211MsoNormal, #yiv5801540211 li.yiv5801540211MsoNormal, #yiv5801540211 div.yiv5801540211MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv5801540211 a:link, #yiv5801540211 span.yiv5801540211MsoHyperlink {color:blue;text-decoration:underline;}#yiv5801540211 p.yiv5801540211msonormal, #yiv5801540211 li.yiv5801540211msonormal, #yiv5801540211 div.yiv5801540211msonormal {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv5801540211 p.yiv5801540211msonormal1, #yiv5801540211 li.yiv5801540211msonormal1, #yiv5801540211 div.yiv5801540211msonormal1 {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv5801540211 span.yiv5801540211ydp1ac82ctlid-translation {}#yiv5801540211 span.yiv5801540211ydpe810003dtlid-translation {}#yiv5801540211 span.yiv5801540211ydpbc4bf220tlid-translation {}#yiv5801540211 span.yiv5801540211ydp44042622tlid-translation {}#yiv5801540211 span.yiv5801540211EmailStyle33 {font-family:sans-serif;color:windowtext;}#yiv5801540211 .yiv5801540211MsoChpDefault {font-size:10.0pt;} _filtered {}#yiv5801540211 div.yiv5801540211WordSection1 {}#yiv5801540211 You need a -s before the “subj1”
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Friday, October 23, 2020 2:44 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 smnfouladi@yahoo.com wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Wednesday, October 21, 2020 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
hi
I want to process MRI images to extractMorphology 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 smnfouladi@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 bfischl@mgh.harvard.edu wrote:
#yiv8204521348 -- filtered {}#yiv8204521348 filtered {}#yiv8204521348 filtered {}#yiv8204521348 p.yiv8204521348MsoNormal, #yiv8204521348 li.yiv8204521348MsoNormal, #yiv8204521348 div.yiv8204521348MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv8204521348 a:link, #yiv8204521348 span.yiv8204521348MsoHyperlink {color:blue;text-decoration:underline;}#yiv8204521348 p.yiv8204521348msonormal, #yiv8204521348 li.yiv8204521348msonormal, #yiv8204521348 div.yiv8204521348msonormal {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv8204521348 p.yiv8204521348msonormal1, #yiv8204521348 li.yiv8204521348msonormal1, #yiv8204521348 div.yiv8204521348msonormal1 {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv8204521348 span.yiv8204521348ydp1ac82ctlid-translation {}#yiv8204521348 span.yiv8204521348ydpe810003dtlid-translation {}#yiv8204521348 span.yiv8204521348ydpbc4bf220tlid-translation {}#yiv8204521348 span.yiv8204521348ydp44042622tlid-translation {}#yiv8204521348 span.yiv8204521348EmailStyle33 {font-family:sans-serif;color:windowtext;}#yiv8204521348 .yiv8204521348MsoChpDefault {font-size:10.0pt;}#yiv8204521348 filtered {}#yiv8204521348 div.yiv8204521348WordSection1 {}#yiv8204521348 You need a -s before the “subj1”
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Friday, October 23, 2020 2:44 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 smnfouladi@yahoo.com wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Wednesday, October 21, 2020 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
hi
I want to process MRI images to extractMorphology 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Saman
That’s really a scientific question and up to you! Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] please help me
External Email - Use Caution 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 <smnfouladi@yahoo.commailto:smnfouladi@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 <bfischl@mgh.harvard.edumailto:bfischl@mgh.harvard.edu> wrote:
You need a -s before the “subj1”
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <smnfouladi@yahoo.commailto:smnfouladi@yahoo.com> wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 bfischl@mgh.harvard.edu wrote:
#yiv6205427093 #yiv6205427093 -- _filtered {} _filtered {} _filtered {}#yiv6205427093 #yiv6205427093 p.yiv6205427093MsoNormal, #yiv6205427093 li.yiv6205427093MsoNormal, #yiv6205427093 div.yiv6205427093MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv6205427093 a:link, #yiv6205427093 span.yiv6205427093MsoHyperlink {color:blue;text-decoration:underline;}#yiv6205427093 p.yiv6205427093msonormal, #yiv6205427093 li.yiv6205427093msonormal, #yiv6205427093 div.yiv6205427093msonormal {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv6205427093 p.yiv6205427093msonormal2, #yiv6205427093 li.yiv6205427093msonormal2, #yiv6205427093 div.yiv6205427093msonormal2 {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv6205427093 p.yiv6205427093msonormal11, #yiv6205427093 li.yiv6205427093msonormal11, #yiv6205427093 div.yiv6205427093msonormal11 {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv6205427093 span.yiv6205427093ydp1ac82ctlid-translation {}#yiv6205427093 span.yiv6205427093ydpe810003dtlid-translation {}#yiv6205427093 span.yiv6205427093ydpbc4bf220tlid-translation {}#yiv6205427093 span.yiv6205427093ydp44042622tlid-translation {}#yiv6205427093 span.yiv6205427093EmailStyle36 {font-family:sans-serif;color:windowtext;}#yiv6205427093 .yiv6205427093MsoChpDefault {font-size:10.0pt;} _filtered {}#yiv6205427093 div.yiv6205427093WordSection1 {}#yiv6205427093 Hi Saman
That’s really a scientific question and up to you! Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Saturday, October 24, 2020 7:17 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 smnfouladi@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 bfischl@mgh.harvard.edu wrote:
You need a -s before the “subj1”
Cheers
Bruce
From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Friday, October 23, 2020 2:44 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 smnfouladi@yahoo.com wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Wednesday, October 21, 2020 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
hi
I want to process MRI images to extractMorphology 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Not sure, cortical thickness maybe?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
External Email - Use Caution 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 <bfischl@mgh.harvard.edumailto:bfischl@mgh.harvard.edu> wrote:
Hi Saman
That’s really a scientific question and up to you! Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <smnfouladi@yahoo.commailto:smnfouladi@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 <bfischl@mgh.harvard.edumailto:bfischl@mgh.harvard.edu> wrote:
You need a -s before the “subj1”
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <smnfouladi@yahoo.commailto:smnfouladi@yahoo.com> wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
hi I found the solution to my problem but the following error occurs
I run in linux command:""""""""""""""""""""""""""""""""""""""""""" aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj1 --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats.txt""""""""""""""""""""""""""""""""""""""""""" but show below error an i can not solve it nix: """"""""""""""""""""""""""""""""""""""""""" File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' """"""""""""""""""""""""""""""""""""""""""" I changed the code and direction several times, but in all cases there is this error. This error also happens to asegstats2table.
The attached image shows my access to folders.
please help me
On Saturday, October 24, 2020, 7:27:18 PM GMT+3:30, saman fouladi smnfouladi@yahoo.com wrote:
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 bfischl@mgh.harvard.edu wrote:
#yiv9070223557 -- filtered {}#yiv9070223557 filtered {}#yiv9070223557 filtered {}#yiv9070223557 p.yiv9070223557MsoNormal, #yiv9070223557 li.yiv9070223557MsoNormal, #yiv9070223557 div.yiv9070223557MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv9070223557 a:link, #yiv9070223557 span.yiv9070223557MsoHyperlink {color:blue;text-decoration:underline;}#yiv9070223557 p.yiv9070223557msonormal, #yiv9070223557 li.yiv9070223557msonormal, #yiv9070223557 div.yiv9070223557msonormal {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv9070223557 p.yiv9070223557msonormal2, #yiv9070223557 li.yiv9070223557msonormal2, #yiv9070223557 div.yiv9070223557msonormal2 {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv9070223557 p.yiv9070223557msonormal11, #yiv9070223557 li.yiv9070223557msonormal11, #yiv9070223557 div.yiv9070223557msonormal11 {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv9070223557 span.yiv9070223557ydp1ac82ctlid-translation {}#yiv9070223557 span.yiv9070223557ydpe810003dtlid-translation {}#yiv9070223557 span.yiv9070223557ydpbc4bf220tlid-translation {}#yiv9070223557 span.yiv9070223557ydp44042622tlid-translation {}#yiv9070223557 span.yiv9070223557EmailStyle36 {font-family:sans-serif;color:windowtext;}#yiv9070223557 .yiv9070223557MsoChpDefault {font-size:10.0pt;}#yiv9070223557 filtered {}#yiv9070223557 div.yiv9070223557WordSection1 {}#yiv9070223557 Hi Saman
That’s really a scientific question and up to you! Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Saturday, October 24, 2020 7:17 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 smnfouladi@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 bfischl@mgh.harvard.edu wrote:
You need a -s before the “subj1”
Cheers
Bruce
From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Friday, October 23, 2020 2:44 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 smnfouladi@yahoo.com wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Wednesday, October 21, 2020 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 bfischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
hi
I want to process MRI images to extractMorphology 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1rIlj-_YicHISrHtnMIutIuvN-YmfuSxpfmlZSaJyBwTe9E...
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1rIlj-_YicHISrHtnMIutIuvN-YmfuSxpfmlZSaJyBwTe9E... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1rIlj-_YicHISrHtnMIutIuvN-YmfuSxpfmlZSaJyBwTe9E...
Hello,
Are you still getting the error message that “atleast 1 subject must be provided”? Or is it a different error message? The screenshot shows you are in the directory MRI4 but the command you’ve sent indicates you want to output aparcstats.txt to the directory team33. Make sure to remove the space in “/home/team33/aparcstats.txt”, and that you have proper permissions to write to the directory ‘team33’.
Cheers, Bill
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of saman fouladi smnfouladi@yahoo.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, November 6, 2020 at 1:13 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] please help me {Disarmed}
External Email - Use Caution hi
I found the solution to my problem but the following error occurs
I run in linux command: """"""""""""""""""""""""""""""""""""""""""" aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj1 --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats.txt """"""""""""""""""""""""""""""""""""""""""" but show below error an i can not solve it nix:
""""""""""""""""""""""""""""""""""""""""""" File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' """""""""""""""""""""""""""""""""""""""""""
I changed the code and direction several times, but in all cases there is this error. This error also happens to asegstats2table.
The attached image shows my access to folders.
please help me
On Saturday, October 24, 2020, 7:27:18 PM GMT+3:30, saman fouladi smnfouladi@yahoo.com wrote:
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 bfischl@mgh.harvard.edu wrote:
Hi Saman
That’s really a scientific question and up to you! Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <smnfouladi@yahoo.commailto:smnfouladi@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 <bfischl@mgh.harvard.edumailto:bfischl@mgh.harvard.edu> wrote:
You need a -s before the “subj1”
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <smnfouladi@yahoo.commailto:smnfouladi@yahoo.com> wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] please help me
External Email - Use Caution
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 <bfischl@mgh.harvard.edumailto:bfischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of saman fouladi Sent: Tuesday, October 20, 2020 4:12 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] please help me
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1rIlj-_YicHISrHtnMIutIuvN-YmfuSxpfmlZSaJyBwTe9E1Mg0LJ7bAG5sCRCVlAwmTsW0mvV3_WEjsaOsXy5wjPJZhXmIlCmAcMx-W6hLW85YfesNoms_k-8XwQZYrNsEaLQpIoSN_VEit_pF-yKz20tdWe6X8gjtQ4noU2_12M3byL1xgyPwavGw-oo6rFKCeAZjlwpj2rwHw905KXTw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1rIlj-_YicHISrHtnMIutIuvN-YmfuSxpfmlZSaJyBwTe9E1Mg0LJ7bAG5sCRCVlAwmTsW0mvV3_WEjsaOsXy5wjPJZhXmIlCmAcMx-W6hLW85YfesNoms_k-8XwQZYrNsEaLQpIoSN_VEit_pF-yKz20tdWe6X8gjtQ4noU2_12M3byL1xgyPwavGw-oo6rFKCeAZjlwpj2rwHw905KXTw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1rIlj-_YicHISrHtnMIutIuvN-YmfuSxpfmlZSaJyBwTe9E1Mg0LJ7bAG5sCRCVlAwmTsW0mvV3_WEjsaOsXy5wjPJZhXmIlCmAcMx-W6hLW85YfesNoms_k-8XwQZYrNsEaLQpIoSN_VEit_pF-yKz20tdWe6X8gjtQ4noU2_12M3byL1xgyPwavGw-oo6rFKCeAZjlwpj2rwHw905KXTw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Also, when you use --subjects, just supply the subject name (subj1), not a path to the subject
On 11/6/2020 11:56 AM, Ammon, William wrote:
Hello,
Are you still getting the error message that “atleast 1 subject must be provided”? Or is it a different error message? The screenshot shows you are in the directory MRI4 but the command you’ve sent indicates you want to output aparcstats.txt to the directory team33.
Make sure to remove the space in “/home/team33/aparcstats.txt”, and that you have proper permissions to write to the directory ‘team33’.
Cheers,
Bill
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of saman fouladi smnfouladi@yahoo.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, November 6, 2020 at 1:13 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] please help me {Disarmed}
* External Email - Use Caution *
hi
I found the solution to my problem but the following error occurs
I run in linux command:
"""""""""""""""""""""""""""""""""""""""""""
aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj1 --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats.txt
"""""""""""""""""""""""""""""""""""""""""""
but show below error an i can not solve it nix:
"""""""""""""""""""""""""""""""""""""""""""
File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided'
"""""""""""""""""""""""""""""""""""""""""""
I changed the code and direction several times, but in all cases there is this error.
This error also happens to asegstats2table.
The attached image shows my accessto folders.
please help me
On Saturday, October 24, 2020, 7:27:18 PM GMT+3:30, saman fouladi smnfouladi@yahoo.com wrote:
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 bfischl@mgh.harvard.edu wrote:
Hi Saman
That’s really a scientific question and up to you! Bruce
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 *Subject:* Re: [Freesurfer] please help me
* External Email - Use Caution *
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 <smnfouladi@yahoo.com mailto:smnfouladi@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 <bfischl@mgh.harvard.edu mailto:bfischl@mgh.harvard.edu> wrote:
You need a -s before the “subj1”
Cheers
Bruce
*From:*freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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
* External Email - Use Caution *
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 <smnfouladi@yahoo.com mailto:smnfouladi@yahoo.com> wrote:
hi Bruce
thank you very very much
On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce <bfischl@mgh.harvard.edu mailto:bfischl@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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
* External Email - Use Caution *
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 <bfischl@mgh.harvard.edu mailto:bfischl@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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
* External Email - Use Caution *
hi
I want to process MRI images to extract Morphologyfeatures.
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1rIlj-_YicHISrHtnMIutIuvN-YmfuSxpfmlZSaJyBwTe9E1Mg0LJ7bAG5sCRCVlAwmTsW0mvV3_WEjsaOsXy5wjPJZhXmIlCmAcMx-W6hLW85YfesNoms_k-8XwQZYrNsEaLQpIoSN_VEit_pF-yKz20tdWe6X8gjtQ4noU2_12M3byL1xgyPwavGw-oo6rFKCeAZjlwpj2rwHw905KXTw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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