External Email - Use Caution
Dhivya,
this syntax works for me with version 6. With version 5.3.0 I am getting the same error mesage. I do not know how the correct syntax is with version 5.3.0. Antonin Skoch
Yep , I am using "o" .I am running it on Ubuntu 16.04 and my freesurfer version is ,
freesurfer/5.3.0/bin/freesurfer
mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz
still I am getting , unknown option --o
Trying to give as per documentation, which is
--o outstem --regheader subject
I am really sorry to bother you with so many questions. Is it something to do with version of freesurfer? ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 11:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run:
mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . .
On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use Cautionmri_compute_volume_fractions --o test --regheader unknown option --o
If I am not giving any input before arguments, it is not taking them.
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 10:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
just run the command as I sent it:
mri_compute_volume_fractions --o test --regheader
the aseg is the default name. You are putting it in the wrong place and it thinks the aseg is a registration file
On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionI am getting same Error with many permutations of arguments,
mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader identity.nofile
arg = 6 reading registration file 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from 002_S/mri/aseg.mgz mri_compute_volume_fractions: could not load registration file from 002_S/mri/aseg.mgz
Thanks, Dhivya
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 6:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
try
mri_compute_volume_fractions --o test --regheader
On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionThanks Bruce!
I even tried with --regheader
mri_compute_volume_fractions mri/aseg.mgz --o test --regheader identity.nofile
It gives me below error,
arg = 6 reading registration file mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from mri/aseg.mgz mri_compute_volume_fractions: could not load registration file from mri/aseg.mgz
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 6:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
oh, this must be Doug's code, not mine. Try using --regheader instead
And also please send us the full command and all screen output from it in the future. cheers Bruce On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionSorry for bothering with more questions!
I am getting an error saying ,
mri_compute_volume_fractions: could not load registration file from identity.nofile
And my command is,
mri_compute_volume_fractions identity.nofile mri/aseg.mgz test
and if I try to give in this format which the documentation says,
mri_compute_volume_fractions [options] --o <outstem> --reg <regfile>
Am I going wrong somewhere?
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 4:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
Hi Dhivya
if you are doing it in the space of the anatomicals, then use identity.nofile as the reg file (which is a special file name that will internally create an identity matrix). The output stem is whatever you pick - it will be prepended to the files that are written with the volume fractions.
cheers Bruce On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionHi,
I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I am not sure about the parameters to supply, <reg file> and <output stem>?
Could Someone point me to some documentation on how should use this function to get the segmentations ?
Thanks, Dhivya
External Email - Use Caution
Thanks Antonin,
I will probably try with version 6.
Thanks, Dhivya ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Antonin Skoch [ansk@ikem.cz] Sent: Thursday, April 26, 2018 1:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_compute_volume_fractions
External Email - Use Caution
Dhivya,
this syntax works for me with version 6. With version 5.3.0 I am getting the same error mesage. I do not know how the correct syntax is with version 5.3.0.
Antonin Skoch
Yep , I am using "o" .
I am running it on Ubuntu 16.04 and my freesurfer version is ,
freesurfer/5.3.0/bin/freesurfer
mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz
still I am getting , unknown option --o
Trying to give as per documentation, which is
--o outstem --regheader subject
I am really sorry to bother you with so many questions. Is it something to do with version of freesurfer? ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 11:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run:
mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . .
On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use Cautionmri_compute_volume_fractions --o test --regheader unknown option --o
If I am not giving any input before arguments, it is not taking them.
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 10:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
just run the command as I sent it:
mri_compute_volume_fractions --o test --regheader
the aseg is the default name. You are putting it in the wrong place and it thinks the aseg is a registration file
On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionI am getting same Error with many permutations of arguments,
mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader identity.nofile
arg = 6 reading registration file 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from 002_S/mri/aseg.mgz mri_compute_volume_fractions: could not load registration file from 002_S/mri/aseg.mgz
Thanks, Dhivya
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 6:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
try
mri_compute_volume_fractions --o test --regheader
On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionThanks Bruce!
I even tried with --regheader
mri_compute_volume_fractions mri/aseg.mgz --o test --regheader identity.nofile
It gives me below error,
arg = 6 reading registration file mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from mri/aseg.mgz mri_compute_volume_fractions: could not load registration file from mri/aseg.mgz
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 6:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
oh, this must be Doug's code, not mine. Try using --regheader instead
And also please send us the full command and all screen output from it in the future. cheers Bruce On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionSorry for bothering with more questions!
I am getting an error saying ,
mri_compute_volume_fractions: could not load registration file from identity.nofile
And my command is,
mri_compute_volume_fractions identity.nofile mri/aseg.mgz test
and if I try to give in this format which the documentation says,
mri_compute_volume_fractions [options] --o <outstem> --reg <regfile>
Am I going wrong somewhere?
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 4:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
Hi Dhivya
if you are doing it in the space of the anatomicals, then use identity.nofile as the reg file (which is a special file name that will internally create an identity matrix). The output stem is whatever you pick - it will be prepended to the files that are written with the volume fractions.
cheers Bruce On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionHi,
I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I am not sure about the parameters to supply, <reg file> and <output stem>?
Could Someone point me to some documentation on how should use this function to get the segmentations ?
Thanks, Dhivya
If you want to run in 5.3, you will need a registration file, which you can generate with
tkregister --mov subject/mri/norm.mgz --s subject --regheader --reg regheader.subject.dat
then something like
mri_compute_volume_fractions regheader.subject.dat subject/mri/pvf
On 4/26/18 5:22 PM, Srinivasan, Dhivya wrote:
External Email - Use CautionThanks Antonin,
I will probably try with version 6.
Thanks, Dhivya ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Antonin Skoch [ansk@ikem.cz] Sent: Thursday, April 26, 2018 1:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_compute_volume_fractions
External Email - Use CautionDhivya,
this syntax works for me with version 6. With version 5.3.0 I am getting the same error mesage. I do not know how the correct syntax is with version 5.3.0.
Antonin Skoch
Yep , I am using "o" .
I am running it on Ubuntu 16.04 and my freesurfer version is ,
freesurfer/5.3.0/bin/freesurfer
mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz
still I am getting , unknown option --o
Trying to give as per documentation, which is
--o outstem --regheader subject
I am really sorry to bother you with so many questions. Is it something to do with version of freesurfer? ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 11:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run:
mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . .
On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use Cautionmri_compute_volume_fractions --o test --regheader unknown option --o
If I am not giving any input before arguments, it is not taking them.
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 10:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
just run the command as I sent it:
mri_compute_volume_fractions --o test --regheader
the aseg is the default name. You are putting it in the wrong place and it thinks the aseg is a registration file
On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionI am getting same Error with many permutations of arguments,
mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader identity.nofile
arg = 6 reading registration file 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from 002_S/mri/aseg.mgz mri_compute_volume_fractions: could not load registration file from 002_S/mri/aseg.mgz
Thanks, Dhivya
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 6:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
try
mri_compute_volume_fractions --o test --regheader
On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionThanks Bruce!
I even tried with --regheader
mri_compute_volume_fractions mri/aseg.mgz --o test --regheader identity.nofile
It gives me below error,
arg = 6 reading registration file mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from mri/aseg.mgz mri_compute_volume_fractions: could not load registration file from mri/aseg.mgz
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 6:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
oh, this must be Doug's code, not mine. Try using --regheader instead
And also please send us the full command and all screen output from it in the future. cheers Bruce On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionSorry for bothering with more questions!
I am getting an error saying ,
mri_compute_volume_fractions: could not load registration file from identity.nofile
And my command is,
mri_compute_volume_fractions identity.nofile mri/aseg.mgz test
and if I try to give in this format which the documentation says,
mri_compute_volume_fractions [options] --o <outstem> --reg <regfile>
Am I going wrong somewhere?
Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 4:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions
Hi Dhivya
if you are doing it in the space of the anatomicals, then use identity.nofile as the reg file (which is a special file name that will internally create an identity matrix). The output stem is whatever you pick - it will be prepended to the files that are written with the volume fractions.
cheers Bruce On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote:
External Email - Use CautionHi,
I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I am not sure about the parameters to supply, <reg file> and <output stem>?
Could Someone point me to some documentation on how should use this function to get the segmentations ?
Thanks, Dhivya
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Antonin Skoch -
Douglas Greve -
Srinivasan, Dhivya