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-boun...@nmr.mgh.harvard.edu> on behalf of saman
fouladi <smnfoul...@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
<smnfoul...@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
<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
<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>
*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
<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
* 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
<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
* 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
<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
* 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
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