Re: [Freesurfer] Question about running recon-all with deface
Hi Bruce, When the thickness/volume measure was compared between the results obtained with recon-all with and without defaced T1 as input to recon-all, we obtained 20% errors (between them) Example: 100*(Thalamus_left_volume_with_defaced_T1_to_recon-all MINUS Thalamus_left_volume_without_deface_T1_to_recon_all)/( thalamus_left_volume_without_deface_T1_to_recon_all) We think, we would rather run recon-all with the face but use -deface flag during recon-all. Thanks Regards Virendra -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, December 14, 2015 10:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question about running recon-all with deface Hi Virenda can you say what you mean by 20% errors? Compared to what? Note for example that a 20% variation in the thickness at one spot would mean a change of 0.4mm (for 2mm thick cortex). Seeing this type of variation point-wise somewhere in the brain isn't terribly surprising, although I wish it were less. Defacing will definitely change things (e.g. skull stripping, bias estimation and removal, etc...) cheers Bruce On Mon, 14 Dec 2015, Mishra, Virendra wrote: > > Hi, > > > > I will appreciate if somebody could reply to my message that was posted > earlier. I copy-paste the message here again. > > > > We are currently in the process of analyzing some data that was > defaced using mri_deface command of freesurfer. This defaced data was > then used as an input to recon-all and the volume and thickness was > computed. These results were then compared against the same subject’s > recon-all with the face but with and without the deface flag within > recon-all. All of the steps were done on version 5.3.0 on CentOS. We have got > some differences and we are unable to explain why. Some of the regions have > error greater than 20% when the input was a defaced brain. We would > appreciate if you could advise as to how to approach to the same results as > we were running the data with the face . > > > > To summarize: (The commands are not precise below but we ensured the > commands are run correctly per the command help) > > 1) Step 1: mri_deface -i original_T1 -o deface_T1 > > 2) Step 2: recon-all -i deface_T1 > > 3) Step 3: recon-all –i original_T1 –deface > > 4) Step 4: recon-all –i original_T1 > > 5) The results from Step 3 is exactly equal to Step 4 > > 6) The results from Step 2 and Step3/4 have errors >20% in certain > regions. > > 7) Step 1-4 are done with version 5.3.0 > > > > Any response will be greatly appreciated. > > > > > > Thanks > > > > Regards > > > > Virendra > > === > > 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 se
Re: [Freesurfer] Question about running recon-all with deface
I see. That is surprisingly large for whole structure volumes. We don't have a lot of experience analyzing defaced volumes, so I would do recon-all on the original data, then deface post-hoc. If you upload one subject where you find a large (or the largest) difference, I'll take alook On Tue, 15 Dec 2015, Mishra, Virendra wrote: Hi Bruce, When the thickness/volume measure was compared between the results obtained with recon-all with and without defaced T1 as input to recon-all, we obtained 20% errors (between them) Example: 100*(Thalamus_left_volume_with_defaced_T1_to_recon-all MINUS Thalamus_left_volume_without_deface_T1_to_recon_all)/( thalamus_left_volume_without_deface_T1_to_recon_all) We think, we would rather run recon-all with the face but use -deface flag during recon-all. Thanks Regards Virendra -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, December 14, 2015 10:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question about running recon-all with deface Hi Virenda can you say what you mean by 20% errors? Compared to what? Note for example that a 20% variation in the thickness at one spot would mean a change of 0.4mm (for 2mm thick cortex). Seeing this type of variation point-wise somewhere in the brain isn't terribly surprising, although I wish it were less. Defacing will definitely change things (e.g. skull stripping, bias estimation and removal, etc...) cheers Bruce On Mon, 14 Dec 2015, Mishra, Virendra wrote: Hi, I will appreciate if somebody could reply to my message that was posted earlier. I copy-paste the message here again. We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject’s recon-all with the face but with and without the deface flag within recon-all. All of the steps were done on version 5.3.0 on CentOS. We have got some differences and we are unable to explain why. Some of the regions have error greater than 20% when the input was a defaced brain. We would appreciate if you could advise as to how to approach to the same results as we were running the data with the face . To summarize: (The commands are not precise below but we ensured the commands are run correctly per the command help) 1) Step 1: mri_deface -i original_T1 -o deface_T1 2) Step 2: recon-all -i deface_T1 3) Step 3: recon-all –i original_T1 –deface 4) Step 4: recon-all –i original_T1 5) The results from Step 3 is exactly equal to Step 4 6) The results from Step 2 and Step3/4 have errors >20% in certain regions. 7) Step 1-4 are done with version 5.3.0 Any response will be greatly appreciated. Thanks Regards Virendra === 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 e
[Freesurfer] Question about running recon-all with deface
Hi, I will appreciate if somebody could reply to my message that was posted earlier. I copy-paste the message here again. We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject's recon-all with the face but with and without the deface flag within recon-all. All of the steps were done on version 5.3.0 on CentOS. We have got some differences and we are unable to explain why. Some of the regions have error greater than 20% when the input was a defaced brain. We would appreciate if you could advise as to how to approach to the same results as we were running the data with the face . To summarize: (The commands are not precise below but we ensured the commands are run correctly per the command help) 1) Step 1: mri_deface -i original_T1 -o deface_T1 2) Step 2: recon-all -i deface_T1 3) Step 3: recon-all -i original_T1 -deface 4) Step 4: recon-all -i original_T1 5) The results from Step 3 is exactly equal to Step 4 6) The results from Step 2 and Step3/4 have errors >20% in certain regions. 7) Step 1-4 are done with version 5.3.0 Any response will be greatly appreciated. Thanks Regards Virendra === 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 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.
Re: [Freesurfer] Question about running recon-all with deface
Hi Virenda can you say what you mean by 20% errors? Compared to what? Note for example that a 20% variation in the thickness at one spot would mean a change of 0.4mm (for 2mm thick cortex). Seeing this type of variation point-wise somewhere in the brain isn't terribly surprising, although I wish it were less. Defacing will definitely change things (e.g. skull stripping, bias estimation and removal, etc...) cheers Bruce On Mon, 14 Dec 2015, Mishra, Virendra wrote: Hi, I will appreciate if somebody could reply to my message that was posted earlier. I copy-paste the message here again. We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject’s recon-all with the face but with and without the deface flag within recon-all. All of the steps were done on version 5.3.0 on CentOS. We have got some differences and we are unable to explain why. Some of the regions have error greater than 20% when the input was a defaced brain. We would appreciate if you could advise as to how to approach to the same results as we were running the data with the face . To summarize: (The commands are not precise below but we ensured the commands are run correctly per the command help) 1) Step 1: mri_deface -i original_T1 -o deface_T1 2) Step 2: recon-all -i deface_T1 3) Step 3: recon-all –i original_T1 –deface 4) Step 4: recon-all –i original_T1 5) The results from Step 3 is exactly equal to Step 4 6) The results from Step 2 and Step3/4 have errors >20% in certain regions. 7) Step 1-4 are done with version 5.3.0 Any response will be greatly appreciated. Thanks Regards Virendra === 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 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] Question about running recon-all with deface
Hello, We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject's recon-all with the face but with and without the deface flag within recon-all. All of the steps were done on version 5.3.0. We have got some differences and we are unable to explain why. Some of the regions have error greater than 20% when the input was a defaced brain. We would appreciate if you could advise as to how to approach to the same results as we were running the data with the face . To summarize: (The commands are not precise below but we ensured the commands are run correctly per the command help) 1) Step 1: mri_deface -i original_T1 -o deface_T1 2) Step 2: recon-all -i deface_T1 3) Step 3: recon-all -i original_T1 -deface 4) Step 4: recon-all -i original_T1 5) The results from Step 3 is exactly equal to Step 4 6) The results from Step 2 and Step3/4 have errors >20% in certain regions. 7) Step 1-4 are done with version 5.3.0 Any response will be greatly appreciated. Thanks Regards Virendra === 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 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.
