Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem.
Do I edit the aseg.mgz file and just label it as none in this region?
Would I use the command tkmedit <subjid> brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
When done do I run recon-all -autorecon2-noaseg -autorecon3?
Thanks, Darren
On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Check the aseg and see if it was labeled ventricle (and make sure it really isn't). You may need to edit the aseg
On Sep 16, 2012, at 5:19 PM, Darren Gitelman d-gitelman@northwestern.edu wrote:
Hi
I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image.
In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed.
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action...
I have checked and these are sulci and not the occipital extent of the lateral ventricle.
Perhaps it is not a problem, or if it is then how to approach fixing it?
Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073
<3809-error.png>
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Yes
On Sep 16, 2012, at 6:13 PM, Darren Gitelman d-gitelman@northwestern.edu wrote:
Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem.
Do I edit the aseg.mgz file and just label it as none in this region?
Would I use the command tkmedit <subjid> brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
When done do I run recon-all -autorecon2-noaseg -autorecon3?
Thanks, Darren
On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Check the aseg and see if it was labeled ventricle (and make sure it really isn't). You may need to edit the aseg
On Sep 16, 2012, at 5:19 PM, Darren Gitelman d-gitelman@northwestern.edu wrote:
Hi
I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image.
In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action...
I have checked and these are sulci and not the occipital extent of the lateral ventricle.
Perhaps it is not a problem, or if it is then how to approach fixing it?
Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073
<3809-error.png> _______________________________________________ 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.
-- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073
The flag -autorecon2-noaseg seems to no longer be used in version 5.1. i.e. ERROR: Flag -autorecon2-noaseg unrecognized.
For edits made to aseg.mgz, could you please let me know what recon-all flags are recommended for version 5.1 for the case described in the email below?
Thanks.
---- On Sun, 16 Sep 2012 16:07:20 -0700 Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote ----
Yes
On Sep 16, 2012, at 6:13 PM, Darren Gitelman <d-gitelman@northwestern.edu> wrote:
Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem.
Do I edit the aseg.mgz file and just label it as none in this region?
Would I use the command tkmedit <subjid> brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
When done do I run recon-all -autorecon2-noaseg -autorecon3?
Thanks, Darren
On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Check the aseg and see if it was labeled ventricle (and make sure it really isn't). You may need to edit the aseg
On Sep 16, 2012, at 5:19 PM, Darren Gitelman <d-gitelman@northwestern.edu> wrote:
Hi
I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image.
In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action...
I have checked and these are sulci and not the occipital extent of the lateral ventricle.
Perhaps it is not a problem, or if it is then how to approach fixing it?
Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073
<3809-error.png> _______________________________________________ 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.
Hi, I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x.
Using:
mri_convert -it siemens -ot mgz 1.IMA test.mgz I get the error message: does not contain a Siemens ASCII header has this file been anonymised? ERROR: cannot unpack mosiacs without ASCII header
The .IMA files have been taken straight from the scanner console.
If I try:
mri_convert -it dicom -ot mgz 1.IMA test.mgz this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA.
Any suggestions on how to convert the Siemens .IMA files correctly?
Thanks, Paul
Not sure if this helps, but you can alter the output orientation using the flag "--out_orientation" followed by LIA (for example). Maybe the input file needs to be in a specific orientation before it can be converted properly.
On Wed, Dec 4, 2013 at 9:56 PM, prasser prasser@zoho.com wrote:
Hi,
I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x.
Using:
mri_convert -it siemens -ot mgz 1.IMA test.mgz
I get the error message:
does not contain a Siemens ASCII header has this file been anonymised?
ERROR: cannot unpack mosiacs without ASCII header
The .IMA files have been taken straight from the scanner console.
If I try:
mri_convert -it dicom -ot mgz 1.IMA test.mgz
this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA.
Any suggestions on how to convert the Siemens .IMA files correctly?
Thanks,
Paul
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.
Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm the correct application of -out_orientation. I would rather let mri_convert handle this from the .IMAs.
Is there any additional information I can provide from from the .IMA header etc that could shed some light on why mri_convert is behaving in this way?
Thanks, Paul
---- On Wed, 04 Dec 2013 22:11:27 -0800 Mark Plantz <markplantz2016@u.northwestern.edu> wrote ----
Not sure if this helps, but you can alter the output orientation using the flag "--out_orientation" followed by LIA (for example). Maybe the input file needs to be in a specific orientation before it can be converted properly.
On Wed, Dec 4, 2013 at 9:56 PM, prasser <prasser@zoho.com> wrote: Hi, I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x.
Using:
mri_convert -it siemens -ot mgz 1.IMA test.mgz I get the error message: does not contain a Siemens ASCII header has this file been anonymised? ERROR: cannot unpack mosiacs without ASCII header
The .IMA files have been taken straight from the scanner console.
If I try:
mri_convert -it dicom -ot mgz 1.IMA test.mgz this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA.
Any suggestions on how to convert the Siemens .IMA files correctly?
Thanks, Paul
_______________________________________________ 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
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.
This may be a known problem. What version of FS are you using and what is your platform? doug
On 12/5/13 3:26 PM, prasser wrote:
Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm the correct application of -out_orientation. I would rather let mri_convert handle this from the .IMAs.
Is there any additional information I can provide from from the .IMA header etc that could shed some light on why mri_convert is behaving in this way?
Thanks, Paul
---- On Wed, 04 Dec 2013 22:11:27 -0800 *Mark Plantz markplantz2016@u.northwestern.edu* wrote ----
Not sure if this helps, but you can alter the output orientation using the flag "--out_orientation" followed by LIA (for example). Maybe the input file needs to be in a specific orientation before it can be converted properly. On Wed, Dec 4, 2013 at 9:56 PM, prasser <prasser@zoho.com <mailto:prasser@zoho.com>> wrote: Hi, I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x. Using: mri_convert -it siemens -ot mgz 1.IMA test.mgz I get the error message: does not contain a Siemens ASCII header has this file been anonymised? ERROR: cannot unpack mosiacs without ASCII header The .IMA files have been taken straight from the scanner console. If I try: mri_convert -it dicom -ot mgz 1.IMA test.mgz this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA. Any suggestions on how to convert the Siemens .IMA files correctly? Thanks, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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
We are using Freesurfer5.3 on os x 10.8.
On 6 Dec 2013, at 2:19 pm, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
This may be a known problem. What version of FS are you using and what is your platform? doug
On 12/5/13 3:26 PM, prasser wrote: Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm the correct application of -out_orientation. I would rather let mri_convert handle this from the .IMAs.
Is there any additional information I can provide from from the .IMA header etc that could shed some light on why mri_convert is behaving in this way?
Thanks, Paul
---- On Wed, 04 Dec 2013 22:11:27 -0800 Mark Plantz markplantz2016@u.northwestern.edu wrote ----
Not sure if this helps, but you can alter the output orientation using the flag "--out_orientation" followed by LIA (for example). Maybe the input file needs to be in a specific orientation before it can be converted properly.
On Wed, Dec 4, 2013 at 9:56 PM, prasser prasser@zoho.com wrote: Hi,
I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x.
Using:
mri_convert -it siemens -ot mgz 1.IMA test.mgz
I get the error message:
does not contain a Siemens ASCII header has this file been anonymised?
ERROR: cannot unpack mosiacs without ASCII header
The .IMA files have been taken straight from the scanner console.
If I try:
mri_convert -it dicom -ot mgz 1.IMA test.mgz
this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA.
Any suggestions on how to convert the Siemens .IMA files correctly?
Thanks,
Paul
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
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
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.
Can you upload a single dicom file to me? One should be enough
On 12/06/2013 04:02 PM, Paul Rasser wrote:
We are using Freesurfer5.3 on os x 10.8.On 6 Dec 2013, at 2:19 pm, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
This may be a known problem. What version of FS are you using and what is your platform? doug
On 12/5/13 3:26 PM, prasser wrote:
Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm the correct application of -out_orientation. I would rather let mri_convert handle this from the .IMAs.
Is there any additional information I can provide from from the .IMA header etc that could shed some light on why mri_convert is behaving in this way?
Thanks, Paul
---- On Wed, 04 Dec 2013 22:11:27 -0800 *Mark Plantz markplantz2016@u.northwestern.edu* wrote ----
Not sure if this helps, but you can alter the output orientation using the flag "--out_orientation" followed by LIA (for example). Maybe the input file needs to be in a specific orientation before it can be converted properly. On Wed, Dec 4, 2013 at 9:56 PM, prasser <prasser@zoho.com <mailto:prasser@zoho.com>> wrote: Hi, I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x. Using: mri_convert -it siemens -ot mgz 1.IMA test.mgz I get the error message: does not contain a Siemens ASCII header has this file been anonymised? ERROR: cannot unpack mosiacs without ASCII header The .IMA files have been taken straight from the scanner console. If I try: mri_convert -it dicom -ot mgz 1.IMA test.mgz this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA. Any suggestions on how to convert the Siemens .IMA files correctly? Thanks, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
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Bruce Fischl -
Darren Gitelman -
Douglas Greve -
Douglas N Greve
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Mark Plantz -
Paul Rasser -
prasser