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?
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
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
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.
- 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?
- 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?
- 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?
- 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
Hi, I am running a retinotopy analysis using fsfast 5.3. The design has 15 TR blank before and after wedge presented for 30 TR with 7 repeats, and ring presented for 24 TR with 7 repeats. Here is my analysis: mkanalysis -s vz -a rtoy.self.rh -fsd bold -fwhm 2 -nskip 15 -TR 1.5 -retinotopy 48 -paradigm rtopy.par. The data doesn't look right. I assume that the analysis does require the stimuli presentation as a full circle, which means that the last 15 TR blank was accounted as the stimuli presentation time. If I am correct, is there simple way to take care of it in mkanalysis-sess? Second, the ring and wedge were presented in different frequency. It seems that the anslysis-sess does not take this into account in the current configration. Is there a way to specify this? Thanks very much for the help. Xiaomin
_______________________________________________ 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.
Neither of these are easily fixable in FSFAST. You can remove the extra time points for the first problem. For the 2nd one, I guess you can do two analyses, one at each frequency, then ignore the one with the wrong frequency
On 08/02/2016 05:55 PM, Xiaomin Yue wrote:
Hi,
I am running a retinotopy analysis using fsfast 5.3. The design has 15 TR blank before and after wedge presented for 30 TR with 7 repeats, and ring presented for 24 TR with 7 repeats. Here is my analysis: mkanalysis -s vz -a rtoy.self.rh -fsd bold -fwhm 2 -nskip 15 -TR 1.5 -retinotopy 48 -paradigm rtopy.par.
The data doesn't look right. I assume that the analysis does require the stimuli presentation as a full circle, which means that the last 15 TR blank was accounted as the stimuli presentation time. If I am correct, is there simple way to take care of it in mkanalysis-sess? Second, the ring and wedge were presented in different frequency. It seems that the anslysis-sess does not take this into account in the current configration. Is there a way to specify this?
Thanks very much for the help.
Xiaomin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
recon-all -autorecon1 -autorecon2 -> no problems
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!
- 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@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.
- 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?
- 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?
- 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?
- 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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@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.
recon-all -autorecon1 -autorecon2 -> no problems
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!
- 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 Wikihttp://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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@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.
- 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?
- 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?
- 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?
- 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ 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@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Silas -
Xiaomin Yue