Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
1. I have done some manual editing of the brainmask for skullstripping, saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
2. For then initial analysis of my data, I would like to create a table of intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl
Hi Cheryl, 1) Yes, just use save not save as 2) this information is already generated and can be found in the aseg.stats in each subject's stats dir. Some of the information is at the top of that file.
On Mon, 31 Jan 2011, Cheryl McCreary wrote:
Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
- I have done some manual editing of the brainmask for skullstripping,
saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
- For then initial analysis of my data, I would like to create a table of
intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Allison,
Is there a way into incorporate these files into the brainmask without having to redo the edits? I processed a number of subjects this way, using 'save main volume as' as directed in the recommended recon workflow.
Thanks,
Cheryl
On 1/31/11 7:05 PM, "Allison Stevens" astevens@nmr.mgh.harvard.edu wrote:
Hi Cheryl,
- Yes, just use save not save as
- this information is already generated and can be found in the
aseg.stats in each subject's stats dir. Some of the information is at the top of that file.
On Mon, 31 Jan 2011, Cheryl McCreary wrote:
Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
- I have done some manual editing of the brainmask for skullstripping,
saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
- For then initial analysis of my data, I would like to create a table of
intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl
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.
I'm not actually sure. What are the files that appeared there?
On Tue, 1 Feb 2011, Cheryl McCreary wrote:
Hi Allison,
Is there a way into incorporate these files into the brainmask without having to redo the edits? I processed a number of subjects this way, using 'save main volume as' as directed in the recommended recon workflow.
Thanks,
Cheryl
On 1/31/11 7:05 PM, "Allison Stevens" astevens@nmr.mgh.harvard.edu wrote:
Hi Cheryl,
- Yes, just use save not save as
- this information is already generated and can be found in the
aseg.stats in each subject's stats dir. Some of the information is at the top of that file.
On Mon, 31 Jan 2011, Cheryl McCreary wrote:
Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
- I have done some manual editing of the brainmask for skullstripping,
saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
- For then initial analysis of my data, I would like to create a table of
intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl
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.
and what wiki page were you following? (some of our wiki pages are no longer used but still exist on the site)
On Tue, 2011-02-01 at 15:59 -0500, Allison Stevens wrote:
I'm not actually sure. What are the files that appeared there?
On Tue, 1 Feb 2011, Cheryl McCreary wrote:
Hi Allison,
Is there a way into incorporate these files into the brainmask without having to redo the edits? I processed a number of subjects this way, using 'save main volume as' as directed in the recommended recon workflow.
Thanks,
Cheryl
On 1/31/11 7:05 PM, "Allison Stevens" astevens@nmr.mgh.harvard.edu wrote:
Hi Cheryl,
- Yes, just use save not save as
- this information is already generated and can be found in the
aseg.stats in each subject's stats dir. Some of the information is at the top of that file.
On Mon, 31 Jan 2011, Cheryl McCreary wrote:
Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
- I have done some manual editing of the brainmask for skullstripping,
saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
- For then initial analysis of my data, I would like to create a table of
intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
For instructions I used the link FS Tutorial/SkullStripFix on http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction
The files that appeared in the subject mri directory were COR-info and COR-001, COR-002 ... COR-256. I assumed that these refer to the number of segments in the 3D MRI volume that was acquired in the coronal direction.
On 2/1/11 2:02 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
and what wiki page were you following? (some of our wiki pages are no longer used but still exist on the site)
On Tue, 2011-02-01 at 15:59 -0500, Allison Stevens wrote:
I'm not actually sure. What are the files that appeared there?
On Tue, 1 Feb 2011, Cheryl McCreary wrote:
Hi Allison,
Is there a way into incorporate these files into the brainmask without having to redo the edits? I processed a number of subjects this way, using 'save main volume as' as directed in the recommended recon workflow.
Thanks,
Cheryl
On 1/31/11 7:05 PM, "Allison Stevens" astevens@nmr.mgh.harvard.edu wrote:
Hi Cheryl,
- Yes, just use save not save as
- this information is already generated and can be found in the
aseg.stats in each subject's stats dir. Some of the information is at the top of that file.
On Mon, 31 Jan 2011, Cheryl McCreary wrote:
Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
- I have done some manual editing of the brainmask for skullstripping,
saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
- For then initial analysis of my data, I would like to create a table
of intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what are the files? Is it COR*? If so, you could mri_convert them to the brainmask. From the mri dir do:
mri_convert . brainmask.mgz
but save the old brainmask first of course.
cheers Bruce
On Tue, 1 Feb 2011, Cheryl McCreary wrote:
Hi Allison,
Is there a way into incorporate these files into the brainmask without having to redo the edits? I processed a number of subjects this way, using 'save main volume as' as directed in the recommended recon workflow.
Thanks,
Cheryl
On 1/31/11 7:05 PM, "Allison Stevens" astevens@nmr.mgh.harvard.edu wrote:
Hi Cheryl,
- Yes, just use save not save as
- this information is already generated and can be found in the
aseg.stats in each subject's stats dir. Some of the information is at the top of that file.
On Mon, 31 Jan 2011, Cheryl McCreary wrote:
Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
- I have done some manual editing of the brainmask for skullstripping,
saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
- For then initial analysis of my data, I would like to create a table of
intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl
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.
More questions regarding aseg.stats ...
Are these results corrected for partial voluming? Are the total GM and WM volumes calculated by summing the segment volumes or using surfaces? Is the cerebellum included in the GM and WM volumes reported in the header of the aseg.stats file? Is ICV reported here the same as eTIV, ie estimated from the talairach transform?
Thanks, Cheryl
On 1/31/11 7:05 PM, "Allison Stevens" astevens@nmr.mgh.harvard.edu wrote:
Hi Cheryl,
- Yes, just use save not save as
- this information is already generated and can be found in the
aseg.stats in each subject's stats dir. Some of the information is at the top of that file.
On Mon, 31 Jan 2011, Cheryl McCreary wrote:
Hi,
I'm new to Freesurfer and am trying to process some data for the first time. I have two questions:
- I have done some manual editing of the brainmask for skullstripping,
saving the edits using 'Save As' and the default names. This seems to create a new group of files separate from the brianmask, in the mri subdirectory. Are these edits incorporated in the brainmask when autorecon2 and autorecon3 are run? I ask because the pial surfaces viewed using tkmedit after processing is complete often extends into the dura and unstripped skull that remains visible on the brainmask, even though it was removed in manual editing. Should I be using 'Save' instead of 'Save as' after editing?
- For then initial analysis of my data, I would like to create a table of
intracranial volume, brain parenchymal volume, gray matter volume and white matter volume. I've tries using the following command line:
mri_segstats --sum TableFileName.sum --pv $SUBJECTS_DIR/Subject/mri/norm.mgz --ctab-default --surf-ctxgmwm --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm
However, this fails with the error: unknown option --surf-ctxgmwm.
What have I missed? Can you recommend another way to get this information? I have also tried asegstats2table as well, but intracranial volume was not included in the table.
Thank you for any assistance or suggestions.
Kind regards, Cheryl
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
-
Allison Stevens -
Bruce Fischl -
Cheryl McCreary -
Nick Schmansky