Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
Hi Douglas,
It seems that the lesions are in the right place. Do you have other suggestions?
I just want to make sure; when you wrote: ind = find( (aseg.vol == 2 | aseg.vol
== 41) & manlesion.vol != 0); -> you meant: ind = find( (aseg.vol == 2 |
aseg.vol == 41) & manlesion.vol ~= 0);
Best, Silas
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Wednesday, August 10, 2016 11:56 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
did you look at the aseg.mgz to see if the lesions were in the right place?
On 08/10/2016 03:28 AM, Silas wrote:
>
> Thank you very much for your help Douglas!
>
>
> I had a few problems running these commands.
>
> 1) recon-all -autorecon1 -autorecon2 -> no problems
>
>
> 2) The matlab script
>
> The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR
> (resliced to 1mm, co-registered in MNI-space and with manually drawn
> binary lesion masks (218x182x182)). I overcome this problem by
> reslicing the FLAIR image and using aseg.auto.nii as the image
> defining space. This was done in SPM8, and prior to this the
> aseg.auto.mgz was converted to a .nii using mri_convert.
>
> This seemed to solve the problem!
>
>
> 3) recon- all -autorecon2-cp -autorecon3
>
> When running the following command i get this error:
>
> /depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS
> -autorecon2-cp -autorecon3 subjid 01MS
>
>
>
>
> '#@# Intensity Normalization2 Mon Aug DATE
> /.../subjects_FLAIR/01MS/mri
>
> mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> using segmentation for initial intensity normalization
> using MR volume brainmask.mgz to mask input volume...
> reading from norm.mgz...
> Reading aseg aseg.mgz
> normalizing image...
> processing with aseg
> removing outliers in the aseg WM...
> 5361 control points removed
> Building bias image
> mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
> building Voronoi diagram...
> Numerical argument out of domain
> Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC
> 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting'
BugReporting - Free Surfer
Wiki<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
surfer.nmr.mgh.harvard.edu
top. Bug Reporting. Submitting a request for help . When submitting a request
for help with your problems please be aware that the developers will try and
repeat your ...
>
> *How can i solve this problem?*
>
>
> Best, Silas
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
> <gr...@nmr.mgh.harvard.edu>
> *Sent:* Tuesday, August 2, 2016 4:06 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
>
> That recon-all command will not work as the FLAIR input should be a
> simple FLAIR image. The FLAIR will only correct the pial surface and
> will have nothing to do with lesion segmentation. Emily Lindermer has
> a tool that can take a T1 and FLAIR and produce a lesion map; but
> given that you already have manual segmentations, maybe that is not so
> helpful. One thing you can do is to edit the aseg.mgz to insert your
> lesions. First run recon-all with -autorecon1 -autorecon2 instead of
> -all. Then, in matlab,
>
>
> aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
>
> manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever
> format, but should be binary
>
> ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);
>
> newaseg = aseg;
>
> newaseg.vol(ind) = 77;
>
> MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so
> make a backup
>
>
> Then run recon-all with -autorecon2-cp -autorecon3
>
>
>
> On 8/1/16 7:35 AM, Silas wrote:
>>
>>
>> Dear FreeSurfer team,
>>
>>
>> I'm doing a structural analysis with 50 MS patients and 50 healthy
>> controls (T1, T2 and FLAIR). The MS patients have multiple lesions
>> mainly in white matter. My co-worker did manual editing (bullet
>> points) in the FLAIR images, and i would like to use these edits when
>> running recon-all in order to avoid further manual editing.
>>
>>
>> The data i'm working
Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
did you look at the aseg.mgz to see if the lesions were in the right place?
On 08/10/2016 03:28 AM, Silas wrote:
>
> Thank you very much for your help Douglas!
>
>
> I had a few problems running these commands.
>
> 1) recon-all -autorecon1 -autorecon2 -> no problems
>
>
> 2) The matlab script
>
> The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR
> (resliced to 1mm, co-registered in MNI-space and with manually drawn
> binary lesion masks (218x182x182)). I overcome this problem by
> reslicing the FLAIR image and using aseg.auto.nii as the image
> defining space. This was done in SPM8, and prior to this the
> aseg.auto.mgz was converted to a .nii using mri_convert.
>
> This seemed to solve the problem!
>
>
> 3) recon- all -autorecon2-cp -autorecon3
>
> When running the following command i get this error:
>
> /depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS
> -autorecon2-cp -autorecon3 subjid 01MS
>
>
>
>
> '#@# Intensity Normalization2 Mon Aug DATE
> /.../subjects_FLAIR/01MS/mri
>
> mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> using segmentation for initial intensity normalization
> using MR volume brainmask.mgz to mask input volume...
> reading from norm.mgz...
> Reading aseg aseg.mgz
> normalizing image...
> processing with aseg
> removing outliers in the aseg WM...
> 5361 control points removed
> Building bias image
> mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
> building Voronoi diagram...
> Numerical argument out of domain
> Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC
> 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting'
>
> *How can i solve this problem?*
>
>
> Best, Silas
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
> <gr...@nmr.mgh.harvard.edu>
> *Sent:* Tuesday, August 2, 2016 4:06 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
>
> That recon-all command will not work as the FLAIR input should be a
> simple FLAIR image. The FLAIR will only correct the pial surface and
> will have nothing to do with lesion segmentation. Emily Lindermer has
> a tool that can take a T1 and FLAIR and produce a lesion map; but
> given that you already have manual segmentations, maybe that is not so
> helpful. One thing you can do is to edit the aseg.mgz to insert your
> lesions. First run recon-all with -autorecon1 -autorecon2 instead of
> -all. Then, in matlab,
>
>
> aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
>
> manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever
> format, but should be binary
>
> ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);
>
> newaseg = aseg;
>
> newaseg.vol(ind) = 77;
>
> MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so
> make a backup
>
>
> Then run recon-all with -autorecon2-cp -autorecon3
>
>
>
> On 8/1/16 7:35 AM, Silas wrote:
>>
>>
>> Dear FreeSurfer team,
>>
>>
>> I'm doing a structural analysis with 50 MS patients and 50 healthy
>> controls (T1, T2 and FLAIR). The MS patients have multiple lesions
>> mainly in white matter. My co-worker did manual editing (bullet
>> points) in the FLAIR images, and i would like to use these edits when
>> running recon-all in order to avoid further manual editing.
>>
>>
>> The data i'm working with is already resliced to 1 mm and
>> co-registered in MNI-space.
>>
>> 1) Can i use this data or would it be preferable to use the original
>> T1's?
>>
>>
>> My thought was to run the following command:
>>
>> recon-all -subject subjectname -i /path/to/input_volume -FLAIR
>> /path/to/FLAIR_volume_with_edits-FLAIRpial -all
>> 2) Does this look correct? Is there anything i should be aware of? ->
>> update: Does this command only improve the pial surface? How can i
>> also improve the white mater segmentation (white) using FLAIR
>> corrections?
>>
>> 3) Does it make a difference running recon-all -all with the FLAIR
>> image - compared to running recon-all -autorecon3 with the FLAIR
>> after running recon-all -all with only the T1?
>>
>> 4) I've also thought about using the lesion s
Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
Thank you very much for your help Douglas!
I had a few problems running these commands.
1) recon-all -autorecon1 -autorecon2 -> no problems
2) The matlab script
The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR
(resliced to 1mm, co-registered in MNI-space and with manually drawn binary
lesion masks (218x182x182)). I overcome this problem by reslicing the FLAIR
image and using aseg.auto.nii as the image defining space. This was done in
SPM8, and prior to this the aseg.auto.mgz was converted to a .nii using
mri_convert.
This seemed to solve the problem!
3) recon- all -autorecon2-cp -autorecon3
When running the following command i get this error:
/depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS -autorecon2-cp
-autorecon3 subjid 01MS
'#@# Intensity Normalization2 Mon Aug DATE
/.../subjects_FLAIR/01MS/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
5361 control points removed
Building bias image
mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
building Voronoi diagram...
Numerical argument out of domain
Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC 2015
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting'
How can i solve this problem?
Best, Silas
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Tuesday, August 2, 2016 4:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
That recon-all command will not work as the FLAIR input should be a simple
FLAIR image. The FLAIR will only correct the pial surface and will have nothing
to do with lesion segmentation. Emily Lindermer has a tool that can take a T1
and FLAIR and produce a lesion map; but given that you already have manual
segmentations, maybe that is not so helpful. One thing you can do is to edit
the aseg.mgz to insert your lesions. First run recon-all with -autorecon1
-autorecon2 instead of -all. Then, in matlab,
aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever format, but
should be binary
ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);
newaseg = aseg;
newaseg.vol(ind) = 77;
MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so make a
backup
Then run recon-all with -autorecon2-cp -autorecon3
On 8/1/16 7:35 AM, Silas wrote:
Dear FreeSurfer team,
I'm doing a structural analysis with 50 MS patients and 50 healthy controls
(T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white
matter. My co-worker did manual editing (bullet points) in the FLAIR images,
and i would like to use these edits when running recon-all in order to avoid
further manual editing.
The data i'm working with is already resliced to 1 mm and co-registered in
MNI-space.
1) Can i use this data or would it be preferable to use the original T1's?
My thought was to run the following command:
recon-all -subject subjectname -i /path/to/input_volume -FLAIR
/path/to/FLAIR_volume_with_edits -FLAIRpial -all
2) Does this look correct? Is there anything i should be aware of? -> update:
Does this command only improve the pial surface? How can i also improve the
white mater segmentation (white) using FLAIR corrections?
3) Does it make a difference running recon-all -all with the FLAIR image -
compared to running recon-all -autorecon3 with the FLAIR after running
recon-all -all with only the T1?
4) I've also thought about using the lesion segmentation toolbox for SPM and
completely avoid manual editing - is this preferable to using the FLAIR with
manual editing?
5) How is the general strength of analysing corpus callosum structurally in MS
patients using FreeSurfer?
Best, Silas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was s
Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR
That recon-all command will not work as the FLAIR input should be a
simple FLAIR image. The FLAIR will only correct the pial surface and
will have nothing to do with lesion segmentation. Emily Lindermer has a
tool that can take a T1 and FLAIR and produce a lesion map; but given
that you already have manual segmentations, maybe that is not so
helpful. One thing you can do is to edit the aseg.mgz to insert your
lesions. First run recon-all with -autorecon1 -autorecon2 instead of
-all. Then, in matlab,
aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever
format, but should be binary
ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);
newaseg = aseg;
newaseg.vol(ind) = 77;
MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so
make a backup
Then run recon-all with -autorecon2-cp -autorecon3
On 8/1/16 7:35 AM, Silas wrote:
Dear FreeSurfer team,
I'm doing a structural analysis with 50 MS patients and 50 healthy
controls (T1, T2 and FLAIR). The MS patients have multiple lesions
mainly in white matter. My co-worker did manual editing (bullet
points) in the FLAIR images, and i would like to use these edits when
running recon-all in order to avoid further manual editing.
The data i'm working with is already resliced to 1 mm and
co-registered in MNI-space.
1) Can i use this data or would it be preferable to use the original T1's?
My thought was to run the following command:
recon-all -subject subjectname -i /path/to/input_volume -FLAIR
/path/to/FLAIR_volume_with_edits-FLAIRpial -all
2) Does this look correct? Is there anything i should be aware of? ->
update: Does this command only improve the pial surface? How can i
also improve the white mater segmentation (white) using FLAIR
corrections?
3) Does it make a difference running recon-all -all with the FLAIR
image - compared to running recon-all -autorecon3 with the FLAIR after
running recon-all -all with only the T1?
4) I've also thought about using the lesion segmentation toolbox for
SPM and completely avoid manual editing - is this preferable to using
the FLAIR with manual editing?
5) How is the general strength of analysing corpus callosum
structurally in MS patients using FreeSurfer?
Best, Silas
___
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
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] Fw: Running recon-all with T1 and FLAIR
Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when running recon-all in order to avoid further manual editing. The data i'm working with is already resliced to 1 mm and co-registered in MNI-space. 1) Can i use this data or would it be preferable to use the original T1's? My thought was to run the following command: recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume_with_edits -FLAIRpial -all 2) Does this look correct? Is there anything i should be aware of? -> update: Does this command only improve the pial surface? How can i also improve the white mater segmentation (white) using FLAIR corrections? 3) Does it make a difference running recon-all -all with the FLAIR image - compared to running recon-all -autorecon3 with the FLAIR after running recon-all -all with only the T1? 4) I've also thought about using the lesion segmentation toolbox for SPM and completely avoid manual editing - is this preferable to using the FLAIR with manual editing? 5) How is the general strength of analysing corpus callosum structurally in MS patients using FreeSurfer? Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
