I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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.
===================================
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Thank you.
===================================
Please consider the environment before printing this e-mail
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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.
===================================
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Thank you.
===================================
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote:
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though.
Thank you! Anna ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label
That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote:
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
-- 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.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect
On 09/29/2016 01:12 PM, Crawford, Anna wrote:
I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though.
Thank you! Anna ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label
That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote:
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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-- 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.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Thank you.
you can also look at the vertex index of the first entry in the label file and type that into the "cursor" field in freeview so it will go to that point. My guess is that it does intersect the surface, otherwise the label indices would have stayed -1
On Thu, 29 Sep 2016, Douglas N Greve wrote:
Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect
On 09/29/2016 01:12 PM, Crawford, Anna wrote:
I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though.
Thank you! Anna ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label
That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote:
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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Please consider the environment before printing this e-mail
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
-- 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.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Thank you.
i used dmax white. I now can see it on the inflated surface. Thank you for all your help in getting this working. Sorry, it took so long since I'm trying to figure all of this out still. The next step will be to take a volume that already has a selected region defined and projecting that region onto the inflated surface which I'm guessing will be somewhat similar to this.
Thanks again, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 1:14 PM To: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu; Crawford, Anna; Anna Crawford Subject: Re: [Freesurfer] Infalted/Label
you can also look at the vertex index of the first entry in the label file and type that into the "cursor" field in freeview so it will go to that point. My guess is that it does intersect the surface, otherwise the label indices would have stayed -1
On Thu, 29 Sep 2016, Douglas N Greve wrote:
Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect
On 09/29/2016 01:12 PM, Crawford, Anna wrote:
I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though.
Thank you! Anna ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label
That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote:
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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.
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
-- 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.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Please consider the environment before printing this e-mail
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Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
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Thank you.
glad it worked out Bruce On Thu, 29 Sep 2016, Crawford, Anna wrote:
i used dmax white. I now can see it on the inflated surface. Thank you for all your help in getting this working. Sorry, it took so long since I'm trying to figure all of this out still. The next step will be to take a volume that already has a selected region defined and projecting that region onto the inflated surface which I'm guessing will be somewhat similar to this.
Thanks again, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 1:14 PM To: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu; Crawford, Anna; Anna Crawford Subject: Re: [Freesurfer] Infalted/Label
you can also look at the vertex index of the first entry in the label file and type that into the "cursor" field in freeview so it will go to that point. My guess is that it does intersect the surface, otherwise the label indices would have stayed -1
On Thu, 29 Sep 2016, Douglas N Greve wrote:
Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect
On 09/29/2016 01:12 PM, Crawford, Anna wrote:
I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though.
Thank you! Anna ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label
That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote:
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
> Hopefully this works better for you. Thank you, > > Anna > > 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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
-- 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.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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It seems as though I did something else wrong. I am guessing it has to do with dmax (I used inflated as my surface) for the --paint option. I had tried 0,1, and dmax as the input to the option. The new label it created only had 1 entry of all zeros which is why I cannot find it on the surface or the volume I would imagine.
Thanks, Anna ________________________________________ 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: Thursday, September 29, 2016 1:13 PM To: Crawford, Anna; Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu; Anna Crawford Subject: Re: [Freesurfer] Infalted/Label
Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect
On 09/29/2016 01:12 PM, Crawford, Anna wrote:
I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though.
Thank you! Anna ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label
That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote:
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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.
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Thank you.
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
-- 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.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
-- 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.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
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
oh, don't use inflated! The sampling uses the surface to look up the location for the sampling. Use white most likely. The vertex index will allow you to see if on the inflated surface without doing anything else
cheers Bruce On Thu, 29 Sep 2016, Crawford, Anna wrote:
It seems as though I did something else wrong. I am guessing it has to do with dmax (I used inflated as my surface) for the --paint option. I had tried 0,1, and dmax as the input to the option. The new label it created only had 1 entry of all zeros which is why I cannot find it on the surface or the volume I would imagine.
Thanks, Anna ________________________________________ 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: Thursday, September 29, 2016 1:13 PM To: Crawford, Anna; Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu; Anna Crawford Subject: Re: [Freesurfer] Infalted/Label
Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect
On 09/29/2016 01:12 PM, Crawford, Anna wrote:
I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though.
Thank you! Anna ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label
That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example
On 09/29/2016 12:38 PM, Crawford, Anna wrote:
This is the output on label2label. The first colum of the created column is -1.
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
Thanks, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label
I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
Hi,
I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong?
Thank you, Anna ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:00 PM To: Crawford, Anna Cc: Anna Crawford; Douglas N. Greve Subject: RE: Infalted/Label
Hi Anna
the label you send me hasn't been sampled onto the surface, which is why it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You can tell this is the case as the first column has all -1. If it had been sampled onto the surface these values would be in [0, nvertices].
Does you newer one have non-zero values in this column?
cheers Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:
It is in the left hemisphere. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 10:38 AM To: Anna Crawford Cc: Crawford, Anna; Douglas N. Greve Subject: Re: Infalted/Label
are the labels lh or rh? On Wed, 28 Sep 2016, Anna Crawford wrote:
Hopefully this works better for you. Thank you,
Anna
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
-- 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.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
-- 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.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
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Crawford, Anna -
Douglas N Greve