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}

 

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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

 

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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 <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.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

 

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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 <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.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

 

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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 <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.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

 

 


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