[Freesurfer] hippocampal subfields
Hi FS experts, I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my 5.3.0 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the 5.3.0 code. Any advice would be very much appreciated. Kind regards and thanks in advance Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] hippocampal subfields
Hi Eugenio, That's brilliant, thanks so much for the quick response. So I will download the v6 code and how do I call the command so that it runs the v6 subfield analysis from the recon_all command? Thanks again for the guidance. Very much appreciated Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 08 May 2015 13:16 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields Hi Erik, the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 module on data analyzed with 5.3, both results will co-exist in the MRI directory of each subject. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message ----- From: "Erik O'Hanlon" To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 2:07:18 PM Subject: [Freesurfer] hippocampal subfields Hi FS experts, I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my 5.3.0 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the 5.3.0 code. Any advice would be very much appreciated. Kind regards and thanks in advance Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippocampal subfields
Hi Eugenio, Sorry, forgot to ask if I can run it with the longitudinal pipeline too? Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 08 May 2015 14:36 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields Hi Eugenio, That's brilliant, thanks so much for the quick response. So I will download the v6 code and how do I call the command so that it runs the v6 subfield analysis from the recon_all command? Thanks again for the guidance. Very much appreciated Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 08 May 2015 13:16 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields Hi Erik, the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 module on data analyzed with 5.3, both results will co-exist in the MRI directory of each subject. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message ----- From: "Erik O'Hanlon" To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 2:07:18 PM Subject: [Freesurfer] hippocampal subfields Hi FS experts, I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my 5.3.0 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the 5.3.0 code. Any advice would be very much appreciated. Kind regards and thanks in advance Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippocampal subfields
That is super Nick, I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6? Thanks again for all the help Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu] Sent: 08 May 2015 19:05 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields Erik, If you wanted to test a 'beta' of v6, which has the new hippocampal stream, then our current internal 'dev' build, which is very close to being the upcoming v6, can be downloaded from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ This goes for anyone else on the list who would like to help us test v6 prior to release. Nick On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote: > Hi Eugenio, > > That's brilliant, thanks so much for the quick response. So I will > download the v6 code and how do I call the command so that it runs the > v6 subfield analysis from the recon_all command? > > Thanks again for the guidance. Very much appreciated > > Cheers > > Erik > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias > [e.igles...@bcbl.eu] > Sent: 08 May 2015 13:16 > To: Freesurfer support list > Subject: Re: [Freesurfer] hippocampal subfields > > Hi Erik, > the 6.0 subfield code won't overwrite your 5.3 results, so if you run > the 6.0 module on data analyzed with 5.3, both results will co-exist > in the MRI directory of each subject. > Kind regards, > /Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > - Original Message - > From: "Erik O'Hanlon" > To: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 8, 2015 2:07:18 PM > Subject: [Freesurfer] hippocampal subfields > > > > Hi FS experts, > > > I completed an analysis including the hippocampal subfield options > using 5.3.0. I understand that the subfield options was then removed > and I noticed that the new rev of the subfield code will be ready for > the v6 FS update. Can I use this code with my 5.3.0 code and if so > what files /dirs will I have to remove and how can I run or rerun it > to get the new subfield measures if it's possible. I would really like > to obtain the subfield measures and am not sure if I can use the > existing measures based on the 5.3.0 code. Any advice would be very > much appreciated. > > > Kind regards and thanks in advance > > > Erik > > Erik O'Hanlon > Postdoctoral researcher > > > > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont, D9, Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.ie > > RCSI DEVELOPING HEALTHCARE LEADERS > WHO MAKE A DIFFERENCE WORLDWIDE > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] hippocampal subfields
Hi FS Experts,
I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 and I encountered the following error in the log file
Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 43: 2675 Killed "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
~
It appears that the process finished prematurely and didn't write out anything in the mri/ dir.
Any pointers how to resolve ? Any help greatly appreciated
Cheers
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
____
From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields
That is super Nick,
I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?
Thanks again for all the help
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
This goes for anyone else on the list who would like to help us test v6
prior to release.
Nick
On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
> Hi Eugenio,
>
> That's brilliant, thanks so much for the quick response. So I will
> download the v6 code and how do I call the command so that it runs the
> v6 subfield analysis from the recon_all command?
>
> Thanks again for the guidance. Very much appreciated
>
> Cheers
>
> Erik
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
> [e.igles...@bcbl.eu]
> Sent: 08 May 2015 13:16
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfields
>
> Hi Erik,
> the 6.0 subfield code won't overwrite your 5.3 results, so if you run
> the 6.0 module on data analyzed with 5.3, both results will co-exist
> in the MRI directory of each subject.
> Kind regards,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Erik O'Hanlon"
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, May 8, 2015 2:07:18 PM
> Subject: [Freesurfer] hippocampal subfields
>
>
>
> Hi FS experts,
>
>
> I completed an analysis including the hippocampal subfield options
> using 5.3.0. I understand that the subfield options was then removed
> and I noticed that the new rev of the subfield code will be ready for
> the v6 FS update. Can I use this code with my 5.3.0 code and if so
> what files /dirs will I have to remove and how can I run or rerun it
> to get the new subfield measures if it's possible. I would really like
> to obtain the subfield measures and am not sure if I can use the
> existing measures based on the 5.3.0 code. Any advice would be very
> much appreciated.
>
>
> Kind regards and thanks in advance
>
>
> Erik
>
> Erik O'Hanlon
> Postdoctoral researcher
>
>
>
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
> ___
> 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 patien
Re: [Freesurfer] hippocampal subfields
Hi Eugenio,
I'm trying to run in on a cluster and I think I have eight cores assigned with 2GB per core. I'm not sure if the process is parallelised though so it could be the case that I have the job running on one of the possible core and only using 2GB of RAM. I can
ask the cluster support team to check but is it possible to run the job across the 8 cores and thus grab the 16GB of RAM or will the code only use the one core and I will have to get the RAM assigned to it to be increased.
Any guidance much appreciated and maybe if you could outline a typical system requirement/setup to run a job. I have 200 subjects so your advice would super.
Thanks again
Cheers
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 26 May 2015 10:33
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory? How much RAM do you have?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
- Original Message -----
From: "Erik O'Hanlon"
To: "Freesurfer support list"
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields
Hi FS Experts,
I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 and I encountered the following error in the log file
Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 43: 2675 Killed "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
~
It appears that the process finished prematurely and didn't write out anything in the mri/ dir.
Any pointers how to resolve ? Any help greatly appreciated
Cheers
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields
That is super Nick,
I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?
Thanks again for all the help
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
This goes for anyone else on the list who would like to help us test v6
prior to release.
Nick
On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
> Hi Eugenio,
>
> That's brilliant, thanks so much for the quick response. So I will
> download the v6 code and how do I call the command so that it runs the
> v6 subfield analysis from the recon_all command?
>
> Thanks again for the guidance. Very much appreciated
>
> Cheers
>
> Erik
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
> [e.igles...@bcbl.eu]
> Sent: 08 May 2015 13:16
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfields
>
> Hi Erik,
> the 6.0 subfield code won't overwrite your 5.3 results, so if you run
> the 6.0 module on data analyzed with 5.3, both results will co-exist
> in the MRI directory of each subject.
> Kind regards,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Erik O'Hanlon"
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, May 8, 2015 2:07:18 PM
> Subject: [Freesurfer] hippocampal subfields
>
>
>
> Hi FS experts,
>
>
> I completed an analysis including the hippocampal subfield options
> using 5.3.0. I understand that the subfield options was then removed
> and I noticed that
Re: [Freesurfer] hippocampal subfields
Hi Eugenio,
I managed to get the subfield code process to run, my cluster wasn't using all the allotted RAM for the job, thank you for all the input. Can I ask how long it typically takes as it appears to have completed in about 30mins and gave me the left and right dirs
with the volume txts etc. Just wanted to be sure before I kick it off on the complete data set.
Thanks again for all the help.
Cheers
Ertik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 26 May 2015 11:25
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi again,
The software requires approximately 10GB of RAM
Cheers
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
- Original Message -----
From: Erik O'Hanlon
To: Freesurfer support list
Sent: Tue, 26 May 2015 12:16:00 +0200 (CEST)
Subject: Re: [Freesurfer] hippocampal subfields
<!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left: #80 2px solid; } -->
Hi Eugenio,
I'm trying to run in on a cluster and I think I have eight cores assigned with 2GB per core. I'm not sure if the process is parallelised though so it could be the case that I have the job running on one of the possible core and only using 2GB of RAM.
I can
ask the cluster support team to check but is it possible to run the job across the 8 cores and thus grab the 16GB of RAM or will the code only use the one core and I will have to get the RAM assigned to it to be increased.
Any guidance much appreciated and maybe if you could outline a typical system requirement/setup to run a job. I have 200 subjects so your advice would super.
Thanks again
Cheers
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 26 May 2015 10:33
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory? How much RAM do you have?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
http://www.jeiglesias.com" target="_blank">www.jeiglesias.com
http://www.bcbl.eu" target="_blank">www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: http://www.bcbl.eu/legal-disclaimer" target="_blank">
www.bcbl.eu/legal-disclaimer>
- Original Message -
From: "Erik O'Hanlon" <erikohan...@rcsi.ie>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields
Hi FS Experts,
I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 and I encountered the following error in the log file
Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 43: 2675 Killed "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
~
It appears that the process finished prematurely and didn't write out anything in the mri/ dir.
Any pointers how to resolve ? Any help greatly appreciated
Cheers
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: http://www.rcsi.ie" target="_blank">www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields
That is super Nick,
I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?
Thanks again for all the help
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very cl
[Freesurfer] T2 voxel size needed for recon_all
Dear Freesurfer experts, I'm wondering if there is a minimum voxel size for the T2 iamge to be included in the recon_all. My T1 is .9mm isotropic but the T2 available is 0.5mmx0.5mmx3mm. Would this voxel size offer any benefit or would it be best just to run the recon_all with only the T1 image. Thanks in advance and apologies for this basic question. Kind regards Erik ___ 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] T2 voxel size needed for recon_all
Thanks Bruce, Much appreciated. Cheers Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 16 January 2017 15:41 To: Freesurfer support list Subject: Re: [Freesurfer] T2 voxel size needed for recon_all Hi Erik it's all empirical, but I would think much over 1.5mm in and direction would make it of limited value Bruce On Mon, 16 Jan 2017, Erik O'Hanlon wrote: > Dear Freesurfer experts, > > I'm wondering if there is a minimum voxel size for the T2 iamge to be > included in the recon_all. My T1 is .9mm isotropic but the T2 available is > 0.5mmx0.5mmx3mm. Would this voxel size offer any benefit or would it be best > just to run the recon_all with only the T1 image. > > Thanks in advance and apologies for this basic question. > > Kind regards > > Erik > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FW: registration difficulty
Dear FS experts, I am running my first FS analysis and I'm trying to register my hippocampal subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have the register.dat file automatically so created this using the bbregister tool and registered B0 image to my orig.mgz. I then used this dat to align my aseg to my diffusion space image and it worked well. The issue is when I try to use it to transform my hippocampal subfield volumes to diffusion space. They just don't line up. Is this due to the different FOV for the subfields? Can anyone advise how to get these volumes to transform correctly? Any help would be greatly appreciated. Thanks Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] FW: registration difficulty
Apologies. forwarded it on now Thanks a million Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty Hi Erik can you cc the list so that others (like Doug!) can respond? thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote: > > Hi Bruce, > > Thanks so much for your reply. As for the specifics of what I have tried, so > rry if it was unclear. > > I have performed the usual T1 based FS cortical and subcortical analysis and > included the -hip_subfields so I also get all the subdivision volumes. I ha > ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo > lumes as masks for the purpose of tractography. I created my diff-to-orig da > t file using bbregister. I then used this in the mri_vol2vol and aligned my > aseg.mgz to my nodif image. This worked really well and I then used fslmaths > to extract out the hippocampus from the aseg2diff. This aligns nicely. I th > en tried to apply the same transformation to my subfield volumes but this di > dn't work. As you suggested, and just to clarify, > > should I now rerun the bbregsiter and create a new dat file for the subfield > volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m > y subfield volume to the orig.mgz and then run a second mri_vol2vol but use > the nodif2orig.dat calculated before and use the nodif image as the --mov fi > le and the registered subfield_2orig.nii as the --targ and use the --inv -- > nearest settings as I want end up with my subfield volumes in diffusion spac > e ? > > So sorry for the confusion, really shows my lack of experience with FS. Just > getting completely mixed up at this stage. > > Again apologies for the lack of clarity and confusion but any pointers offer > ed would be fantastic. > > Thanks again > > best regards > > Erik > > __ > > Hi Erik > > so you had a separate (presumably highres) acquisition within the > hippocampus? Have you registered that with bbregister? Your best bet is > probably doing so, then composing the two registrations (and inverting one, > depending on what direction you want to go). > > cheers > Bruce > > > > On Wed, 2 Apr 2014, Erik O'Hanlon wrote: > > > > > > > Dear FS experts, > > > > I am running my first FS analysis and I'm trying to register my hippocampa > l > > subdivision volumes to my diffusion space image but cannot get good > > alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th > e > > register.dat file automatically so created this using the bbregister tool > and > > registered B0 image to my orig.mgz. I then used this dat to align my aseg > to > > my diffusion space image and it worked well. The issue is when I try to us > e > > it to transform my hippocampal subfield volumes to diffusion space. They j > ust > > don't line up. Is this due to the different FOV for the subfields? Can any > one > > advise how to get these volumes to transform correctly? > > > > Any help would be greatly appreciated. > > > > Thanks > > > > Erik > > Dr. Erik O'Hanlon PhD MSc BScEng > Post Doctoral Researcher > > [IMAGE] > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont, D9, Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.ie > > RCSI DEVELOPING HEALTHCARE LEADERS > WHO MAKE A DIFFERENCE WORLDWIDE > > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FW: registration difficulty
Hi Doug, Thanks for that, I will give that a shot and see how it looks. As for my highres hippo images, I ran the recon-all with the -hippo-subfields setting on my T1 highres whole brain anatomy file. This gave me the usual FS outputs and the extra hippo subfield volumes. I can look at these with Freeview and when I load the anatomy, the aseg and the hippo subfields, everything is fine. I then want to transform these to my diffusion space for tractography, and managed to get the anat and aseg images to align with my diffusion space B0 image but just can't get the subfields to align. I think this is due to the smaller fov of the subfields as they appear a small cubes with the hippo structures inside in the Freeview screen. Thanks again for the direction, I haven't tried the tkregister2 tool so I'll play with it and see Much appreciated. best regards Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty >>should I now rerun the bbregsiter and create a new dat file for the subfield >> volume to orig.mgz image? I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface. but I might not understand what is going on ... doug On 04/02/2014 03:03 PM, Erik O'Hanlon wrote: > Apologies. > > forwarded it on now > > Thanks a million > > Erik > > Dr. Erik O'Hanlon PhD MSc BScEng > Post Doctoral Researcher > > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont, D9, Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.ie > > RCSI DEVELOPING HEALTHCARE LEADERS > WHO MAKE A DIFFERENCE WORLDWIDE > ____ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: 02 April 2014 19:58 > To: Erik O'Hanlon > Subject: Re: [Freesurfer] FW: registration difficulty > > Hi Erik > > can you cc the list so that others (like Doug!) can respond? > > thanks > Bruce > On Wed, 2 Apr > 2014, Erik O'Hanlon wrote: > >> Hi Bruce, >> >> Thanks so much for your reply. As for the specifics of what I have tried, so >> rry if it was unclear. >> >> I have performed the usual T1 based FS cortical and subcortical analysis and >> included the -hip_subfields so I also get all the subdivision volumes. I ha >> ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo >> lumes as masks for the purpose of tractography. I created my diff-to-orig da >> t file using bbregister. I then used this in the mri_vol2vol and aligned my >> aseg.mgz to my nodif image. This worked really well and I then used fslmaths >> to extract out the hippocampus from the aseg2diff. This aligns nicely. I th >> en tried to apply the same transformation to my subfield volumes but this di >> dn't work. As you suggested, and just to clarify, >> >> should I now rerun the bbregsiter and create a new dat file for the subfield >> volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m >> y subfield volume to the orig.mgz and then run a second mri_vol2vol but use >> the nodif2orig.dat calculated before and use the nodif image as the --mov fi >> le and the registered subfield_2orig.nii as the --targ and use the --inv -- >> nearest settings as I want end up with my subfield volumes in diffusion spac >> e ? >> >> So sorry for the confusion, really shows my lack of experience with FS. Just >> getting completely mixed up at this stage. >> >> Again apologies for the lack of clarity and confusion but any pointers offer >> ed would be fantastic. >> >> Thanks again >> >> best regards >> >> Erik >> >> ______ >> >> Hi Erik >> >> so you had a separate (presu
Re: [Freesurfer] FW: registration difficulty
Hi Doug, I managed to get the subfield volumes aligned at last. I used bbregister to get the dat file for the No_diff2orig transform. Then used tkregister2 to get the dat for my subfield volume to orig. Used mdi_vol2vol to align my subfield vol to the orig.mgz. Finally aligned the subfieldaligned_orig file to the No_diff image using mdi_vol2vol with the regsiterNodiff2orig.dat file and the --inv flag. I know it's probably not the best way to do it but it all aligns nicely. Thanks for the pointers Cheers Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 03 April 2014 10:23 To: Freesurfer support list Subject: Re: [Freesurfer] FW: registration difficulty Hi Doug, Thanks for that, I will give that a shot and see how it looks. As for my highres hippo images, I ran the recon-all with the -hippo-subfields setting on my T1 highres whole brain anatomy file. This gave me the usual FS outputs and the extra hippo subfield volumes. I can look at these with Freeview and when I load the anatomy, the aseg and the hippo subfields, everything is fine. I then want to transform these to my diffusion space for tractography, and managed to get the anat and aseg images to align with my diffusion space B0 image but just can't get the subfields to align. I think this is due to the smaller fov of the subfields as they appear a small cubes with the hippo structures inside in the Freeview screen. Thanks again for the direction, I haven't tried the tkregister2 tool so I'll play with it and see Much appreciated. best regards Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty >>should I now rerun the bbregsiter and create a new dat file for the subfield >> volume to orig.mgz image? I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface. but I might not understand what is going on ... doug On 04/02/2014 03:03 PM, Erik O'Hanlon wrote: > Apologies. > > forwarded it on now > > Thanks a million > > Erik > > Dr. Erik O'Hanlon PhD MSc BScEng > Post Doctoral Researcher > > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont, D9, Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.ie > > RCSI DEVELOPING HEALTHCARE LEADERS > WHO MAKE A DIFFERENCE WORLDWIDE > ____ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: 02 April 2014 19:58 > To: Erik O'Hanlon > Subject: Re: [Freesurfer] FW: registration difficulty > > Hi Erik > > can you cc the list so that others (like Doug!) can respond? > > thanks > Bruce > On Wed, 2 Apr > 2014, Erik O'Hanlon wrote: > >> Hi Bruce, >> >> Thanks so much for your reply. As for the specifics of what I have tried, so >> rry if it was unclear. >> >> I have performed the usual T1 based FS cortical and subcortical analysis and >> included the -hip_subfields so I also get all the subdivision volumes. I ha >> ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo >> lumes as masks for the purpose of tractography. I created my diff-to-orig da >> t file using bbregister. I then used this in the mri_vol2vol and aligned my >> aseg.mgz to my nodif image. This worked really well and I then used fslmaths >> to extract out the hippocampus from the aseg2diff. This aligns nicely. I th >> en tried to apply the same transformation to my subfield volumes but this di >> dn't work.
[Freesurfer] Hippocampus visualisation
Hi Freesurfer experts, I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all the subfields given in the table output? Sorry for the basic question, just trying to put together some images. Thanks in advance erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] Hippocampus visualisation
That's super Eugenio, Thanks so much. Exactly what I needed. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 02 October 2015 10:57 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampus visualisation Hi Erik, one possible way of doing this: 1. For a single subfield: set the color map to Lookup Table. Tick "show as isosurface in 3d view". Tick "label volume". Then, set both values of the range to the numeric code of the subfield you want to display (e.g., for CA1, it would be 206). 2. For all subfields simultaneously: same as before, but setting the range to 200-226. This will color each subfield differently. 3. For showing the whole hippocampus in the same color: an easy, quick way is to switch the color map to grayscale, tick "show as isosurface in 3d view", untick "label volume", and set the lower and upper thresholds to 200 and 226, respectively. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Erik O'Hanlon" To: "Freesurfer support list" Sent: Friday, October 2, 2015 10:31:17 AM Subject: [Freesurfer] Hippocampus visualisation Hi Freesurfer experts, I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all the subfields given in the table output? Sorry for the basic question, just trying to put together some images. Thanks in advance erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Hi Experts,
Just flowing on from Joe's question, I have run my analysis without the T2 or FLAIR flag but have specificed the T2 which is a FLAIR image for the hippocampal subfield options. I have used
recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair
Should I have used -hippocampal-subfields-T1FLAIR instead? Can I change this and simply rerun without the need to do everything from scratch.
I have T2 and FLAIR images that I havent used for pial correction, can I add that in too and if so which is best teh T2 or the FLAIR or both?
Thanks and as always, really appreciate the help
Cheers
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joe Necus (PGR) [j.nec...@newcastle.ac.uk]
Sent: 03 February 2017 10:56
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.
Joe
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl
Sent: 02 February 2017 22:56
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)
Hi Joe
there are slight differences, and for sure we reserve the right to use
the knowledge that it is a FLAIR scan in the algorithms, so you should
probably rerun
cheers
Bruce
On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:
>
> Hello,
>
>
> I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether
> there is any difference between using the -T2 -T2Pial and -Flair flags.
>
>
> I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and
> would like to know whether I need to go back and instead re-run with the -FLAIR flag instead.
>
>
> Thanks a lot,
>
> Joe
>
>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University
mail.nmr.mgh.harvard.edu
To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
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
MailScanner has detected a possible fraud attempt from "www.partners.org" claiming to be
mycompliancereport.com
www.partners.org
ComplianceLine engages in the business of providing 24-hour toll-free hotlines for the reporting and tracking of compliance concerns to assist in the identification of possible unethical, illegal or questionable behavior.
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Thanks Bruce,
Much appreciated
Best regards
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 03 February 2017 15:18
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags
(freesurfer v6) {Disarmed}
Hi Erik
Eugenio can confirm, but I don't think the subfield stuff cares. The
-hippocampal-subfields-T1T2 means use multiple inputs, but it doesn't
assume anything about the distribution of intensities in them.
cheers
Bruce
On Fri, 3 Feb
2017, Erik O'Hanlon wrote:
> Hi Experts,
>
> Just flowing on from Joe's question, I have run my analysis without the T2 or
> FLAIR flag but have
> specificed the T2 which is a FLAIR image for the hippocampal subfield
> options. I have used
>
> recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2
> /sub008/sub_008_T2.nii.gz T2Flair
>
> Should I have used -hippocampal-subfields-T1FLAIR instead? Can I change this
> and simply rerun without
> the need to do everything from scratch.
> I have T2 and FLAIR images that I havent used for pial correction, can I add
> that in too and if so which
> is best teh T2 or the FLAIR or both?
>
> Thanks and as always, really appreciate the help
>
> Cheers
>
> Erik
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joe
> Necus (PGR) [j.nec...@newcastle.ac.uk]
> Sent: 03 February 2017 10:56
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags
> (freesurfer v6) {Disarmed}
>
> Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.
>
>
> Joe
>
>
>
> Erik O'Hanlon
> Postdoctoral researcher
>
> [IMAGE]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
>
>
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Bruce
> Fischl
> Sent: 02 February 2017 22:56
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags
> (freesurfer v6)
> Hi Joe
>
> there are slight differences, and for sure we reserve the right to use
> the knowledge that it is a FLAIR scan in the algorithms, so you should
> probably rerun
>
> cheers
> Bruce
> On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:
>
> >
> > Hello,
> >
> >
> > I am running recon-all on the latest version of freesurfer (Version 6) and
> > would like to know whether
> > there is any difference between using the -T2 -T2Pial and -Flair flags.
> >
> >
> > I am currently running recon-all with a T1 and FLAIR image, but have used
> > the -T2 -T2pial flags and
> > would like to know whether I need to go back and instead re-run with the
> > -FLAIR flag instead.
> >
> >
> > Thanks a lot,
> >
> > Joe
> >
> >
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> Freesurfer Info Page - Harvard University
> mail.nmr.mgh.harvard.edu
> To see the collection of prior postings to the list, visit the Freesurfer
> Archives. A searchable archive
> which of messages PRIOR to March 2004 is at ...
>
>
>
>
> 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
> MailScanner has detected a possible fraud attempt from "www.partners.org"
> claiming to be
> mycompliancereport.com
> www.partners.org
> ComplianceLine engages in the business of providing 24-hour toll-free
> hotlines for the reporting and
> tracking of compliance concerns to assist in the identification of possible
> unethical, illegal or
> questionable behavior.
>
>
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Thanks for the clarification Eugenio,
Much appreciated
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk]
Sent: 03 February 2017 15:59
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
Hi!
recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair
looks good. The flag -hippocampal-subfields-T1FLAIR does not even exist ;-)
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 3 Feb 2017, at 11:32, Erik O'Hanlon <erikohan...@rcsi.ie> wrote:
recon-all
-all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair
___
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] new Amygdala and Hippocampus segmentation
Hi FS experts, I have run an analysis using v6.0 and included the hippocampal subfields in the command using combined T1 and Flair segmentation. I would now like to look at the Amygdala segementation as described on the FS wiki. I would like to once again use both by T1 and FLAIR images but am a little confused about how to do that. Does the new tool haev to be run for T1 images and then followed by a second T2 specific run? for example would the following generate the hippocampus and amygdala meassures and generate a txt file for each hierarchy (ie HBT.txt, FS60.txt and CA.txt for hippoSF and amygNuc) ? segmentHA_T2.sh subject001 subject001_Flair.nni.gz T1andFlair USE_T1 /subject001 Will this overwrite any of my FS6.0 subfield measures present in the subject MRI dir? Thanks for any help you can provide . Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] new Amygdala and Hippocampus segmentation
Hi Eugenio, Thanks so much for you input. I think I get it now. so I will run the following to get a multispectral segmentation using both T1 and T2Flair? segmentHA_T2.sh /projects/freesurfer/subjects/sub001 /projects//freesurfer/subjects/sub001_T2.nii.gz HippoAMYT1andT2 1 sub001 Just as a quick aside, I'm not sure if my FS 6.0 contains the necessary options to run the Amygdala stuff. Is there an easy way I can check this and if I dont have the correct tool can I simply ad that to my FS build? Thanks again and as always, very much appreciate your help. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 08 December 2017 14:29 To: Freesurfer support list Subject: Re: [Freesurfer] new Amygdala and Hippocampus segmentation Hi Erik, You can runsegmentHA_T2.sh on your FS processed subjects. You don’t need to run segmentHA_T1.sh first. The choice is whether you want to use T1+FLAIR (USE_T1=1) or only FLAIR (USE_T1=0). This command will generate outputs for both hippocampus and amygdala. The output will include multiple segmentations at different hierarchies, but only one text file with all the volumes. Regarding your old 6.0 measures: they’re safe because they used the suffix v10, and the new ones use the suffix v20 Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 8 December 2017 at 14:15 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] new Amygdala and Hippocampus segmentation Hi FS experts, I have run an analysis using v6.0 and included the hippocampal subfields in the command using combined T1 and Flair segmentation. I would now like to look at the Amygdala segementation as described on the FS wiki. I would like to once again use both by T1 and FLAIR images but am a little confused about how to do that. Does the new tool haev to be run for T1 images and then followed by a second T2 specific run? for example would the following generate the hippocampus and amygdala meassures and generate a txt file for each hierarchy (ie HBT.txt, FS60.txt and CA.txt for hippoSF and amygNuc) ? segmentHA_T2.sh subject001 subject001_Flair.nni.gz T1andFlair USE_T1 /subject001 Will this overwrite any of my FS6.0 subfield measures present in the subject MRI dir? Thanks for any help you can provide . Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] new Amygdala and Hippocampus segmentation
Thanks Eugenio, I'll do that. Again very much appreciate your guidance. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 08 December 2017 16:46 To: Freesurfer support list Subject: Re: [Freesurfer] new Amygdala and Hippocampus segmentation Command looks good! But I’d replace HippoAMYT1andT2 by something that reflects the fact that you’re using a FLAIR scan ;-) Regarding the 2nd question: try running segmentHA_T2.sh. If it’s not there, you’ll need a more recent (dev) version. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 8 December 2017 at 14:41 To: Freesurfer support list Subject: Re: [Freesurfer] new Amygdala and Hippocampus segmentation Hi Eugenio, Thanks so much for you input. I think I get it now. so I will run the following to get a multispectral segmentation using both T1 and T2Flair? segmentHA_T2.sh /projects/freesurfer/subjects/sub001 /projects//freesurfer/subjects/sub001_T2.nii.gz HippoAMYT1andT2 1 sub001 Just as a quick aside, I'm not sure if my FS 6.0 contains the necessary options to run the Amygdala stuff. Is there an easy way I can check this and if I dont have the correct tool can I simply ad that to my FS build? Thanks again and as always, very much appreciate your help. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 08 December 2017 14:29 To: Freesurfer support list Subject: Re: [Freesurfer] new Amygdala and Hippocampus segmentation Hi Erik, You can runsegmentHA_T2.sh on your FS processed subjects. You don’t need to run segmentHA_T1.sh first. The choice is whether you want to use T1+FLAIR (USE_T1=1) or only FLAIR (USE_T1=0). This command will generate outputs for both hippocampus and amygdala. The output will include multiple segmentations at different hierarchies, but only one text file with all the volumes. Regarding your old 6.0 measures: they’re safe because they used the suffix v10, and the new ones use the suffix v20 Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 8 December 2017 at 14:15 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] new Amygdala and Hippocampus segmentation Hi FS experts, I have run an analysis using v6.0 and included the hippocampal subfields in the command using combined T1 and Flair segmentation. I would now like to look at the Amygdala segementation as described on the FS wiki. I would like to once again use both by T1 and FLAIR images but am a little confused about how to do that. Does the new tool haev to be run for T1 images and then followed by a second T2 specific run? for example would the following generate the hippocampus and amygdala meassures and generate a txt file for each hierarchy (ie HBT.txt, FS60.txt and CA.txt for hippoSF and amygNuc) ? segmentHA_T2.sh subject001 subject001_Flair.nni.gz T1andFlair USE_T1 /subject001 Will this overwrite any of my FS6.0 subfield measures present in the subject MRI dir? Thanks for any help you can provide . Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] making masks with subfields etc
Hi FS experts, I have run a hippocampal analysis with v6.0 including the subfields and am now in the process of running an addtional analysis using the dev6.0 version for the amygdala and posterior/anterior hippocampal measures. I also want to use the 3D rendered volumes of the hippocampus and amygdala as volume ROI masks for tractography. 1. My diffusion data is registered to my T1 data. Just wondering is it the rawavg.mgz file I need to register the ROI's to? 2. I'm using freeview and 3D rendererd the Hippocampus (203-226) and saved that as a volume. Do I use the mri_vol2vol command to align my roi's to the rawavg image for correctly map onto my T1 native space image because when I try that it seems that the ROI volume image can't be opened. I think I must be missing a step when creating the mask perhaps? 3. If I also wish to generate additional masks from the aseg.mgz, will that be done via the same steps used for the hippocampus or do I need to use the fslmaths -thr LUT number of the subcorical structure -uthr lut number again first and then regsiter them to the rawavg.mzg? Thanks for any guidance which is always greatly appreciated. Best regards Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] making masks with subfields etc
Hello Eugenio, Thanks for your reply. When I'm in freeview, the hippocampus and even the amgydala from the aseg align nicely with my input T1 image. I suspect that it could be an issue when export ing them from freeview. I just saved the hippocampus etc as nii volumes and then tried to open them in FSL view with my T1 which has my DWI image aligned but it complains about image size and dimensions etc which made me think that the hippocampus volumes etc weren't in the same space as my T1. So my files in the subject/mri dir (T1, aseg and hippo etc) are all in native space (the same space that my initial T1 image fed into reconall is in)? Sorry for the confusion on my part. Also as an aside, teh hippocampal subfield measures in the txt files giving the volume for each subfield, are they in mm3 or if my T1 is 0.89mm3 do I need to adjust for that. Thanks again for any help. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 12 January 2018 14:21 To: Freesurfer support list Subject: Re: [Freesurfer] making masks with subfields etc Dear Erik, I might be missing something here, but: the subfield segmentation, rawavg.mgz, etc, are all already in native subject space… Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 12 January 2018 at 13:07 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] making masks with subfields etc Hi FS experts, I have run a hippocampal analysis with v6.0 including the subfields and am now in the process of running an addtional analysis using the dev6.0 version for the amygdala and posterior/anterior hippocampal measures. I also want to use the 3D rendered volumes of the hippocampus and amygdala as volume ROI masks for tractography. 1. My diffusion data is registered to my T1 data. Just wondering is it the rawavg.mgz file I need to register the ROI's to? 2. I'm using freeview and 3D rendererd the Hippocampus (203-226) and saved that as a volume. Do I use the mri_vol2vol command to align my roi's to the rawavg image for correctly map onto my T1 native space image because when I try that it seems that the ROI volume image can't be opened. I think I must be missing a step when creating the mask perhaps? 3. If I also wish to generate additional masks from the aseg.mgz, will that be done via the same steps used for the hippocampus or do I need to use the fslmaths -thr LUT number of the subcorical structure -uthr lut number again first and then regsiter them to the rawavg.mzg? Thanks for any guidance which is always greatly appreciated. Best regards Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] making masks with subfields etc
Brillant. Thanks Eugenio. I'll use the voxel files. Cheers and enjoy the weekend Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 12 January 2018 15:41 To: Freesurfer support list Subject: Re: [Freesurfer] making masks with subfields etc OK, got it. The problem is that your images are aligned in physical coordinates, but not in voxel coordinates. FreeView handles that nicely, but I don’t know about FSLview. The subfield code also generates files named *.FSvoxelSpace.mgz, which are in the same voxel coordinates as the recon-all files. You can try using those instead. Regarding the voxel size of your T1s: the volumes are always in cubic millimeters ;-) Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 12 January 2018 at 15:13 To: Freesurfer support list Subject: Re: [Freesurfer] making masks with subfields etc Hello Eugenio, Thanks for your reply. When I'm in freeview, the hippocampus and even the amgydala from the aseg align nicely with my input T1 image. I suspect that it could be an issue when export ing them from freeview. I just saved the hippocampus etc as nii volumes and then tried to open them in FSL view with my T1 which has my DWI image aligned but it complains about image size and dimensions etc which made me think that the hippocampus volumes etc weren't in the same space as my T1. So my files in the subject/mri dir (T1, aseg and hippo etc) are all in native space (the same space that my initial T1 image fed into reconall is in)? Sorry for the confusion on my part. Also as an aside, teh hippocampal subfield measures in the txt files giving the volume for each subfield, are they in mm3 or if my T1 is 0.89mm3 do I need to adjust for that. Thanks again for any help. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 12 January 2018 14:21 To: Freesurfer support list Subject: Re: [Freesurfer] making masks with subfields etc Dear Erik, I might be missing something here, but: the subfield segmentation, rawavg.mgz, etc, are all already in native subject space… Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 12 January 2018 at 13:07 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] making masks with subfields etc Hi FS experts, I have run a hippocampal analysis with v6.0 including the subfields and am now in the process of running an addtional analysis using the dev6.0 version for the amygdala and posterior/anterior hippocampal measures. I also want to use the 3D rendered volumes of the hippocampus and amygdala as volume ROI masks for tractography. 1. My diffusion data is registered to my T1 data. Just wondering is it the rawavg.mgz file I need to register the ROI's to? 2. I'm using freeview and 3D rendererd the Hippocampus (203-226) and saved that as a volume. Do I use the mri_vol2vol command to align my roi's to the rawavg image for correctly map onto my T1 native space image because when I try that it seems that the ROI volume image can't be opened. I think I must be missing a step when creating the mask perhaps? 3. If I also wish to generate additional masks from the aseg.mgz, will that be done via the same steps used for the hippocampus or do I need to use the fslmaths -thr LUT number of the subcorical structure -uthr lut number again first and then regsiter them to the rawavg.mzg? Thanks for any guidance which is always greatly appreciated. Best regards Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] Hippocampal and amygdala analysis with dev6 FS
Hi FS experts, I've been running into numerous issues trying to run the new amygdala and hippocampal analysis. I processed my data with v6.0 and obtained the 12 subfield measures with the v6.0. I have tried to add the new amygdala and subfield measures from the dev verion but am now getting the following error (see below). I'm running my analysis on a clutser. Any pointers on how to reslve the issue would be very much appreciated. Thanks Erik # #@# Hippocampal Subfields processing (T1+T2) left Fri Jan 26 20:00:15 GMT 2018 -- Setting up environment variables --- LD_LIBRARY_PATH is .:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//runtime/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//bin/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//sys/os/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/lib/vtk/lib/vtk-5.6:/home/support/apps/libs/qwt/6.1.3/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/vtk/5.10.1/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/Python/2.7.12/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/tcl/8.5.19/lib:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//sys/opengl/lib/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/lib/vtk/lib/vtk-5.6:/home/support/apps/libs/qwt/6.1.3/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/vtk/5.10.1/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/Python/2.7.12/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/tcl/8.5.19/lib Invalid MEX-file '/tmp/MCR_2152662503/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64': /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/MCR_2152662503/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64) Error in kvlClear (line 11) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 135) MATLAB:invalidMEXFile @#@FSTIME 2018:01:26:20:00:15 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 29.68 S 1.22 U 11.13 P 41% M 844112 F 2 R 51746 W 0 c 95 w 9198 I 304 O 83584 L 0.00 0.00 0.00 @#@FSLOADPOST 2018:01:26:20:00:45 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 0.39 0.09 0.03 Linux lonsdale-n148.cluster 2.6.32-696.18.7.el6.x86_64 #1 SMP Wed Jan 3 19:31:16 CST 2018 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Fri Jan 26 20:00:45 GMT 2018 Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] Longitudinal errors, Voxel size differs
External Email - Use Caution Hi FS Experts, I'm trying to run a longitudinal analysis across three timepoints and have run the cross steps for the data. I then ran the base step but found that my voxel dimensions are slightly different across the timepoints and I got the following error ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(2) = 0.881117, 0.881117, 0.881117 size(0) = 0.884507, 0.884507, 0.884507 MultiRegistration::loadMovables: voxel size is different /projects/pi-vokeane/HPC_16_00925/MC_FS_testdata_EOH/freesurfer/subjects/abd025_tp3/mri/norm.mgz. I assume I need to resample the data to the voxel size of the first time point and then rerun. Can you advise on what command to use to resample the images from time 2 and time 3 to those of time 1 before rerunning from scratch. I assume I can't avoid rerunning the initial reconall step once I resample my data. Any guidance is much appreciated Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal errors, Voxel size differs
External Email - Use Caution Thank Martin, I've been looking into this and it appears that the slight changes in the sequence may have occurred software updates to the scanner. So essentially from what you say, this drastically impacts any longitudinal analyses as there will be a systematic bias across the data. Is there any point in trying to do longitudinal analyses with such data as it will be a factor in all output? Is it worth resampling all three time points to 1mm and then rerun the analysis as it will be difficult to say if any patterns of change arent due to the acquistions as you said? If I want to resample the data to a "standard 1mm3" voxel size, is there a FS command for that or should I use something in FSL or AFNI tools and then feed the resampled data back to the recon-all inistial step in FS. Thanks for the help and guidance. Much appreciated Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter Sent: 15 May 2018 23:39 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal errors, Voxel size differs Hi Erik, you should investigate why this is the case. Any difference in acquisition will cause effects and it will be impossible to distinguish these from real effects. Also you should never just resample one time point, as that will introduce processing bias. I would advise to - find out why, and you need to report this in any analysis so that people are aware of this potential bias - resample both time points to some 3rd space. Probably here simply conform them to 1mm isotropic. Best, Martin Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] On 15. May 2018, at 07:20, Erik O'Hanlon mailto:erikohan...@rcsi.ie>> wrote: Hi FS Experts, I'm trying to run a longitudinal analysis across three timepoints and have run the cross steps for the data. I then ran the base step but found that my voxel dimensions are slightly different across the timepoints and I got the following error ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(2) = 0.881117, 0.881117, 0.881117 size(0) = 0.884507, 0.884507, 0.884507 MultiRegistration::loadMovables: voxel size is different /projects/pi-vokeane/HPC_16_00925/MC_FS_testdata_EOH/freesurfer/subjects/abd025_tp3/mri/norm.mgz. I assume I need to resample the data to the voxel size of the first time point and then rerun. Can you advise on what command to use to resample the images from time 2 and time 3 to those of time 1 before rerunning from scratch. I assume I can't avoid rerunning the initial reconall step once I resample my data. Any guidance is much appreciated Best regards Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie<mailto:erikohan...@rcsi.ie> W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] hippo subfields and amygdala
External Email - Use Caution Hi FS experts, I have run my analysis using the dev version and have all the necessary volume.txt files. As a secondary step, I want to use some of the subfields as seed volumes for tractography (using ExploreDTI). I have may diffusion data in the same space as the FS brain.mgz but am wondering how I should make the subfield masks so that they will be in the same coordinate space when exported as a nii file. If I use Freeview and load the brain.mgz and then the subfield volumes, is it simply a case of reducing the LUT to the specific subfield and then save that as a volume/mask ? Will that mask be in the same coordinate space and regsitered the brain.nii too. Is it just a matter of doing this process numerous times in Freeview and each time simply changing the LUT corresponding to the specific ROI needed to get the masks I want to use for each subject. Thanks for any information you can offer Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippo subfields and amygdala
External Email - Use Caution Hi Eugenio, Thanks, I'll give that a try. Just a quick question, the correct ROI id's for each subfield are in the LUT ? Is there a different LUT in the DEV version for the hippo and Amy subdivisions individually and also the anterior /posterior divisions and are there different numbers for each hemisphere? If I use the MRI_segment_Label can I make a mask for the whole structure volumes for the hippo and Amy just by listing all the ID's i.e. mri_segment lh.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz 7001 7003 7005 7006 7007 7008 7009 7010 7015 LeftAmygdala.nii Thanks again Eugenio really appreciate the help Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 29 May 2018 11:44:41 To: Freesurfer support list Subject: Re: [Freesurfer] hippo subfields and amygdala External Email - Use Caution Hi Erik, The subfield module gives you a segmentation in the same space as brain.mgz and the rest of volumes in the recon-all stream: [lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz You can use mri_extract_label to create binary masks. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] Reply-To: Freesurfer support list Date: Tuesday, 29 May 2018 at 11:07 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] hippo subfields and amygdala External Email - Use Caution Hi FS experts, I have run my analysis using the dev version and have all the necessary volume.txt files. As a secondary step, I want to use some of the subfields as seed volumes for tractography (using ExploreDTI). I have may diffusion data in the same space as the FS brain.mgz but am wondering how I should make the subfield masks so that they will be in the same coordinate space when exported as a nii file. If I use Freeview and load the brain.mgz and then the subfield volumes, is it simply a case of reducing the LUT to the specific subfield and then save that as a volume/mask ? Will that mask be in the same coordinate space and regsitered the brain.nii too. Is it just a matter of doing this process numerous times in Freeview and each time simply changing the LUT corresponding to the specific ROI needed to get the masks I want to use for each subject. Thanks for any information you can offer Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:image001.png@01D3F742.70D780F0] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:image002.png@01D3F742.70D780F0] ___ 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] hippo subfields and amygdala
External Email - Use Caution Thanks a mill Eugenio, Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 29 May 2018 13:02:07 To: Freesurfer support list Subject: Re: [Freesurfer] hippo subfields and amygdala External Email - Use Caution Yes the LUT evolves but remains backwards compatible. And yes, the command looks OK to me! Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] Reply-To: Freesurfer support list Date: Tuesday, 29 May 2018 at 13:00 To: Freesurfer support list Subject: Re: [Freesurfer] hippo subfields and amygdala External Email - Use Caution Hi Eugenio, Thanks, I'll give that a try. Just a quick question, the correct ROI id's for each subfield are in the LUT ? Is there a different LUT in the DEV version for the hippo and Amy subdivisions individually and also the anterior /posterior divisions and are there different numbers for each hemisphere? If I use the MRI_segment_Label can I make a mask for the whole structure volumes for the hippo and Amy just by listing all the ID's i.e. mri_segment lh.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz 7001 7003 7005 7006 7007 7008 7009 7010 7015 LeftAmygdala.nii Thanks again Eugenio really appreciate the help Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 29 May 2018 11:44:41 To: Freesurfer support list Subject: Re: [Freesurfer] hippo subfields and amygdala External Email - Use Caution Hi Erik, The subfield module gives you a segmentation in the same space as brain.mgz and the rest of volumes in the recon-all stream: [lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz You can use mri_extract_label to create binary masks. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Erik O'Hanlon Postdoctoral researcher [cid:image001.png@01D3F74D.423505F0] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:image002.png@01D3F74D.423505F0] Reply-To: Freesurfer support list Date: Tuesday, 29 May 2018 at 11:07 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] hippo subfields and amygdala External Email - Use Caution Hi FS experts, I have run my analysis using the dev version and have all the necessary volume.txt files. As a secondary step, I want to use some of the subfields as seed volumes for tractography (using ExploreDTI). I have may diffusion data in the same space as the FS brain.mgz but am wondering how I should make the subfield masks so that they will be in the same coordinate space when exported as a nii file. If I use Freeview and load the brain.mgz and then the subfield volumes, is it simply a case of reducing the LUT to the specific subfield and then save that as a volume/mask ? Will that mask be in the same coordinate space and regsitered the brain.nii too. Is it just a matter of doing this process numerous times in Freeview and each time simply changing the LUT corresponding to the specific ROI needed to get the masks I want to use for each subject. Thanks for any information you can offer Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:image003.png@01D3F74D.423505F0] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:image004.png@01D3F74D.423505F0] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard
[Freesurfer] creating a mask for the thalamus parcellations
External Email - Use Caution Dear FS Experts, Is it possible to use the labels found in the FreesurferColourLUT.txt for the Thalamus parcellations (8001-8014) using the mri_extract_label command? If so, what is the correct input file to use ? mri_extract_label 8001 L_Ant_thalamus.mgz Thanks Cheers Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] creating a mask for the thalamus parcellations
External Email - Use Caution Thanks Bruce and Eugenio. it will be great to have so looking forward to it. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 31 May 2018 17:53:26 To: Freesurfer support list Subject: Re: [Freesurfer] creating a mask for the thalamus parcellations External Email - Use Caution I probably shouldn’t say this, but I will, anyway: It’s coming soon! -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 31/05/2018, 17:46, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: not yet, sorry. We are working on it Bruce On Thu, 31 May 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Dear FS Experts, > > > Is it possible to use the labels found in the FreesurferColourLUT.txt for the Thalamus parcellations (8001-8014) using the mri_extract_label command? If so, what is the correct input file to use ? > > > mri_extract_label 8001 L_Ant_thalamus.mgz > > > Thanks > > > Cheers > > > Erik > > Erik O'Hanlon > Postdoctoral researcher > > [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont D9 Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > > > Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > > > RCSI LEADING THE WORLD TO BETTER HEALTH > > [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] creating a mask for the thalamus parcellations
External Email - Use Caution Hi FS Experts again, Would it be possible to use an MNI Thalamus mask from FSL and possibly register it to my FS brain using FS ? I know it won't be based on the subject anatomy and should probably be smoothed to account for inter subject variability. Would this be vastly inferior to the subject specific way, realising that the subdivisions of theThalamus isn't available yet? Thanks and regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon Sent: 01 June 2018 12:35:55 To: Freesurfer support list Subject: Re: [Freesurfer] creating a mask for the thalamus parcellations External Email - Use Caution Thanks Bruce and Eugenio. it will be great to have so looking forward to it. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 31 May 2018 17:53:26 To: Freesurfer support list Subject: Re: [Freesurfer] creating a mask for the thalamus parcellations External Email - Use Caution I probably shouldn’t say this, but I will, anyway: It’s coming soon! -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 31/05/2018, 17:46, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: not yet, sorry. We are working on it Bruce On Thu, 31 May 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Dear FS Experts, > > > Is it possible to use the labels found in the FreesurferColourLUT.txt for the Thalamus parcellations (8001-8014) using the mri_extract_label command? If so, what is the correct input file to use ? > > > mri_extract_label 8001 L_Ant_thalamus.mgz > > > Thanks > > > Cheers > > > Erik > > Erik O'Hanlon > Postdoctoral researcher > > [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont D9 Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > > > Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > > > RCSI LEADING THE WORLD TO BETTER HEALTH > > [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Extract the entorhinal cortex as a mask
External Email - Use Caution Hi FS experts , I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward Thanks for any advice Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extract the entorhinal cortex as a mask
External Email - Use Caution Hi Bruce, Thanks. So if I use the following command mri_extract_Label aparc+aseg.mgz 216 EC.mgz would that give me both L and right EC extracted? is there any way to get the left and right separately? Thanks so much for the help cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 12 June 2018 14:56:41 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask Hi Erik yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC as a volume mask cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Hi FS experts , > > > I'd like to make masks for the entorhinal cortex to use for tractography. Can > you advise what FS tool should be used? I've used the mri_extract_label for > my hippocampal masks but not sure what files to use to extract EC ? I'm sure > it's straightforward > > > Thanks for any advice > > > Best regards > > > Erik > > Erik O'Hanlon > Postdoctoral researcher > > [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont D9 Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > > > Transforming Healthcare Education, Research and Service: RCSI Strategic Plan > 2018-2022<http://www.rcsi.ie/strategy2018> > > > RCSI LEADING THE WORLD TO BETTER HEALTH > > [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extract the entorhinal cortex as a mask
External Email - Use Caution Sorry Bruce, Yep Thanks. I didn't spot that label just the 216. Worked perfectly. Thanks again Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 12 June 2018 19:04:32 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask I think you can use 1006 (left) and 2006 (right) cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Hi Bruce, > > > Thanks. So if I use the following command > > mri_extract_Label aparc+aseg.mgz 216 EC.mgz > > would that give me both L and right EC extracted? is there any way to get the > left and right separately? > > > Thanks so much for the help > > > cheers > > > Erik > Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 12 June 2018 14:56:41 > To: Freesurfer support list > Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask > > Hi Erik > > yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC > as a volume mask > > cheers > Bruce > On Tue, 12 Jun 2018, Erik O'Hanlon wrote: > >>External Email - Use Caution >> >> Hi FS experts , >> >> >> I'd like to make masks for the entorhinal cortex to use for tractography. >> Can you advise what FS tool should be used? I've used the mri_extract_label >> for my hippocampal masks but not sure what files to use to extract EC ? I'm >> sure it's straightforward >> >> >> Thanks for any advice >> >> >> Best regards >> >> >> Erik >> >> Erik O'Hanlon >> Postdoctoral researcher >> >> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] >> >> RCSI Psychiatry >> Royal College of Surgeons in Ireland >> Beaumont Road, Beaumont D9 Ireland >> T: 8093740 >> E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> >> >> >> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan >> 2018-2022<http://www.rcsi.ie/strategy2018> >> >> >> RCSI LEADING THE WORLD TO BETTER HEALTH >> >> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > Erik O'Hanlon > Postdoctoral researcher > > [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont D9 Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > > > Transforming Healthcare Education, Research and Service: RCSI Strategic Plan > 2018-2022<http://www.rcsi.ie/strategy2018> > > > RCSI LEADING THE WORLD TO BETTER HEALTH > > [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal errors, Voxel size differs
External Email - Use Caution Thank you so much Martin. This is super and very much appreciated. I'll try this and resample all my data and then hopefully it will run successfully through the longitudinal pipeline over my three time points. Best regards and again thank you for your reply. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter Sent: 04 July 2018 16:32:41 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal errors, Voxel size differs Hi Erik, better late then never: you should use mri_convert --conform input output Best, Martin Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] On 16. May 2018, at 12:19, Erik O'Hanlon mailto:erikohan...@rcsi.ie>> wrote: External Email - Use Caution Thank Martin, I've been looking into this and it appears that the slight changes in the sequence may have occurred software updates to the scanner. So essentially from what you say, this drastically impacts any longitudinal analyses as there will be a systematic bias across the data. Is there any point in trying to do longitudinal analyses with such data as it will be a factor in all output? Is it worth resampling all three time points to 1mm and then rerun the analysis as it will be difficult to say if any patterns of change arent due to the acquistions as you said? If I want to resample the data to a "standard 1mm3" voxel size, is there a FS command for that or should I use something in FSL or AFNI tools and then feed the resampled data back to the recon-all inistial step in FS. Thanks for the help and guidance. Much appreciated Erik From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Martin Reuter mailto:mreu...@nmr.mgh.harvard.edu>> Sent: 15 May 2018 23:39 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal errors, Voxel size differs Hi Erik, you should investigate why this is the case. Any difference in acquisition will cause effects and it will be impossible to distinguish these from real effects. Also you should never just resample one time point, as that will introduce processing bias. I would advise to - find out why, and you need to report this in any analysis so that people are aware of this potential bias - resample both time points to some 3rd space. Probably here simply conform them to 1mm isotropic. Best, Martin Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie<mailto:erikohan...@rcsi.ie> W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE On 15. May 2018, at 07:20, Erik O'Hanlon mailto:erikohan...@rcsi.ie>> wrote: Hi FS Experts, I'm trying to run a longitudinal analysis across three timepoints and have run the cross steps for the data. I then ran the base step but found that my voxel dimensions are slightly different across the timepoints and I got the following error ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(2) = 0.881117, 0.881117, 0.881117 size(0) = 0.884507, 0.884507, 0.884507 MultiRegistration::loadMovables: voxel size is different /projects/pi-vokeane/HPC_16_00925/MC_FS_testdata_EOH/freesurfer/subjects/abd025_tp3/mri/norm.mgz. I assume I need to resample the data to the voxel size of the first time point and then rerun. Can you advise on what command to use to resample the images from time 2 and time 3 to those of time 1 before rerunning from scratch. I assume I can't avoid rerunning the initial reconall step once I resample my data. Any guidance is much appreciated Best regards Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie<mailto:erikohan...@rcsi.ie> W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI DEVELOPING HEAL
[Freesurfer] Longitudinal analysis and hippocampal subfields
Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-logob489c8] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie<mailto:erikohan...@rcsi.ie> W: www.rcsi.ie<http://www.rcsi.ie> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] Longitudinal analysis and hippocampal subfields
Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:part1.06080901.05020203@nmr.mgh.harvard.edu] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie<mailto:erikohan...@rcsi.ie> W: www.rcsi.ie<http://www.rcsi.ie> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu> reu...@mit.edu<mailto:reu...@mit.edu> Web : http://reuter.mit.edu ___ 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] Longitudinal analysis and hippocampal subfields
That's super! Thanks again Martin Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 18:07 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:part1.06060905.0900@nmr.mgh.harvard.edu] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie<mailto:erikohan...@rcsi.ie> W: www.rcsi.ie<http://www.rcsi.ie> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu> reu...@mit.edu<mailto:reu...@mit.edu> Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu> reu...@mit.edu<mailto:reu...@mit.edu> Web : http://reuter.mit.edu ___ 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] Longitudinal analysis and hippocampal subfields
Hi Martin, I appear to have run into an issue when processing longitudinal data with the -hippo-subfields command. I get the following error. I have run the process in the cross (independent) mode and it ran okay at each time point (I have two). Wrote out aseg_thresholded.mgz kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 imageFileName: aseg_thresholded.mgz radius: 3 Using dilating filter itk::ExceptionObject (0x2ccf4d0) Location: "void itk::ImageFileWriter::Write() [with TInputImage = main(int, char**)::ImageType]" File: /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileWriter.txx Line: 271 Description: itk::ERROR: ImageFileWriter(0x2cb8880): Largest possible region does not fully contain requested paste IO regionPaste$ Dimension: 3 Index: 0 0 0 Size: 0 0 0 Largest possible region: ImageRegion (0x7fff9c9b02e0) Dimension: 3 Index: [0, 0, 0] Size: [0, 0, 0] failed to do kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 Linux tcin-n08.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub040_tp1.long.sub040_T1_baseimage exited with ERRORS at Wed Nov 19 20:34:12 GMT 2014 For more details, see the log file /projects/pi-frodlt/HPC_11_00383/Freesurfer_ABD/sub040_tp1.long.sub040_T1_baseimage$ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas very much appreciated. Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 18 November 2014 20:42 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields That's super! Thanks again Martin Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 18:07 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:part1.06060905.0900@nmr.mgh.harvard.edu] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie<mailto:erikohan...@rcsi.ie> W: www.rcsi.ie<http://www.rcsi.ie> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu> reu...@mit.edu<mailto:reu...@mit.edu> Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr
Re: [Freesurfer] Longitudinal analysis and hippocampal subfields
Sorry, forgot to say that I tried the -long option for two time points without the -hippo-subields option and it completed without errors. Thanks again Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 20 November 2014 13:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Martin, I appear to have run into an issue when processing longitudinal data with the -hippo-subfields command. I get the following error. I have run the process in the cross (independent) mode and it ran okay at each time point (I have two). Wrote out aseg_thresholded.mgz kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 imageFileName: aseg_thresholded.mgz radius: 3 Using dilating filter itk::ExceptionObject (0x2ccf4d0) Location: "void itk::ImageFileWriter::Write() [with TInputImage = main(int, char**)::ImageType]" File: /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileWriter.txx Line: 271 Description: itk::ERROR: ImageFileWriter(0x2cb8880): Largest possible region does not fully contain requested paste IO regionPaste$ Dimension: 3 Index: 0 0 0 Size: 0 0 0 Largest possible region: ImageRegion (0x7fff9c9b02e0) Dimension: 3 Index: [0, 0, 0] Size: [0, 0, 0] failed to do kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 Linux tcin-n08.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub040_tp1.long.sub040_T1_baseimage exited with ERRORS at Wed Nov 19 20:34:12 GMT 2014 For more details, see the log file /projects/pi-frodlt/HPC_11_00383/Freesurfer_ABD/sub040_tp1.long.sub040_T1_baseimage$ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas very much appreciated. Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 18 November 2014 20:42 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields That's super! Thanks again Martin Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 18:07 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:part1.06060905.0900@nmr.mgh.harvard.edu] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie<mailto:erikohan...@rcsi.ie> W: www.rcsi.ie<http://www.rcsi.ie> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martino
Re: [Freesurfer] Longitudinal analysis and hippocampal subfields
Hi Eugenio, Should I send the files via dropbox, as it appears that the last one I sent is waiting approval due to size etc. Thanks and sorry for the hassle Erik From: Erik O'Hanlon Sent: 20 November 2014 15:51 To: Freesurfer support list Subject: RE: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Eugenio, Yes, it seems to have happened on a few cases, I've only started running it with the subfields and the jobs are running on a cluster so many have not run to end yet but al that have, exit with the error. I've attached the hippo_subfields-log you requested. As the other subfieldResults is quite large with subdirs, should I sent you a dropbox link? Thanks for help. Very much appreciated, Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 20 November 2014 14:47 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, did you experience the same problem with any other cases? Also, do you think you could send us the log file [subjectdir]/scripts/hippo-subfields.log, as well as the contents of [subjectdir]/tmp/subrieldResults? Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message ----- From: "Erik O'Hanlon" To: "Freesurfer support list" Sent: Thursday, November 20, 2014 2:04:15 PM Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Martin, I appear to have run into an issue when processing longitudinal data with the -hippo-subfields command. I get the following error. I have run the process in the cross (independent) mode and it ran okay at each time point (I have two). Wrote out aseg_thresholded.mgz kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 imageFileName: aseg_thresholded.mgz radius: 3 Using dilating filter itk::ExceptionObject (0x2ccf4d0) Location: "void itk::ImageFileWriter::Write() [with TInputImage = main(int, char**)::ImageType]" File: /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileWriter.txx Line: 271 Description: itk::ERROR: ImageFileWriter(0x2cb8880): Largest possible region does not fully contain requested paste IO regionPaste$ Dimension: 3 Index: 0 0 0 Size: 0 0 0 Largest possible region: ImageRegion (0x7fff9c9b02e0) Dimension: 3 Index: [0, 0, 0] Size: [0, 0, 0] failed to do kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 Linux tcin-n08.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub040_tp1.long.sub040_T1_baseimage exited with ERRORS at Wed Nov 19 20:34:12 GMT 2014 For more details, see the log file /projects/pi-frodlt/HPC_11_00383/Freesurfer_ABD/sub040_tp1.long.sub040_T1_baseimage$ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas very much appreciated. Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 18 November 2014 20:42 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields That's super! Thanks again Martin Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 18:07 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu ] on behalf of Martin Reuter [ mreu...@nmr.mgh.harvard.edu ] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfi
Re: [Freesurfer] Hippocampal subfields
Hi FS experts, Yes, I'm in the same position and have been trying to do it longitudinally. Does this mean that the outputs are completely unreliable and unstable? Should it be parked until the release of version 6? Thanks Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of angela.fav...@unipd.it [angela.fav...@unipd.it] Sent: 02 December 2014 21:53 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields Hi all, this is really a terrible news! I am writing a paper using hippocampal subfields (ver 5.3). What is the problem with segmentation using this tool? Is it reliable at least on some of the subfield? When will Freesurfer 6 be released? Thank you Angela > Hi Georg, > we will be releasing with FreeSurfer 6 a new hippocampal subfield module > based on a more accurate atlas built upon ex vivo MRI scans. However, if > what you are interested in is the whole hippocampal volume, the results > from the new module won't be too different. > Cheers, > /Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > - Original Message - > From: "Georg Ferdinand Anto von Polier" > To: "Freesurfer support list" > Sent: Tuesday, December 2, 2014 2:46:40 PM > Subject: [Freesurfer] Hippocampal subfields > > > > > > Dear FreeSurfers, > > > > I am just finishing a paper using output from Hippocampal subfields and > recognized that the current version has been deprecated. I am interested > in volumes of the whole hippocampus. > > Are these volumes still valid and can you estimate when a new version will > be available? Can you provide maybe a brief comment on the decision to > deprecate the current version? > > Best regards, > > Georg > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Using the new Thalamus tool
External Email - Use Caution Hi FS Experts I've run my data through the brainstem, hippocampus and amygdala following the usual Recon_all and using the developmental version downloaded and stalled around Jan2018. I'd like to use the new thalamus tool and am wondering if I need to do a full install of the latest DEV version to do so. As I am still working on certain aspects of the analyses I've run so far, I don't want to overwrite my main FS installation mid analysis. Is it possible to download the toolbox and add it to my current dev version or is it best just to do another install with teh complete new Dev version? Is it possible to run the Thalamus analysis as an addtional component without having to rerun the recon_all again? Thanks and regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Using the new Thalamus tool
External Email - Use Caution Thanks Eugenio, I'll intall the latest dev version so. How long does it typically take to run a subject through the thalamus pipeline typically? Thanks again for the prompt reply. Very much appreciated. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 10 September 2018 18:00:20 To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list Subject: Re: [Freesurfer] Using the new Thalamus tool External Email - Use Caution Dear Erik, Installing only the thalamic tool is technically possible but requires a level of hacking that i don't want to encourage or support ;-) Please install the new dev on a separate directory, and make FREESURFER_HOME point to that the directory (and source freesurfer) to run the thalamic tool. No need to rerun recon-all on the subjects. Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon Sent: Thursday, September 6, 2018 3:44:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Using the new Thalamus tool External Email - Use Caution Hi FS Experts I've run my data through the brainstem, hippocampus and amygdala following the usual Recon_all and using the developmental version downloaded and stalled around Jan2018. I'd like to use the new thalamus tool and am wondering if I need to do a full install of the latest DEV version to do so. As I am still working on certain aspects of the analyses I've run so far, I don't want to overwrite my main FS installation mid analysis. Is it possible to download the toolbox and add it to my current dev version or is it best just to do another install with teh complete new Dev version? Is it possible to run the Thalamus analysis as an addtional component without having to rerun the recon_all again? Thanks and regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Using the new Thalamus tool
External Email - Use Caution That's super. Thanks again Eugenio, Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 11 September 2018 16:44:34 To: Freesurfer support list; Freesurfer support list Subject: Re: [Freesurfer] Using the new Thalamus tool External Email - Use Caution 10-15 mins or so Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon Sent: Tuesday, September 11, 2018 12:32:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Using the new Thalamus tool External Email - Use Caution Thanks Eugenio, I'll intall the latest dev version so. How long does it typically take to run a subject through the thalamus pipeline typically? Thanks again for the prompt reply. Very much appreciated. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 10 September 2018 18:00:20 To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list Subject: Re: [Freesurfer] Using the new Thalamus tool External Email - Use Caution Dear Erik, Installing only the thalamic tool is technically possible but requires a level of hacking that i don't want to encourage or support ;-) Please install the new dev on a separate directory, and make FREESURFER_HOME point to that the directory (and source freesurfer) to run the thalamic tool. No need to rerun recon-all on the subjects. Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon Sent: Thursday, September 6, 2018 3:44:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Using the new Thalamus tool External Email - Use Caution Hi FS Experts I've run my data through the brainstem, hippocampus and amygdala following the usual Recon_all and using the developmental version downloaded and stalled around Jan2018. I'd like to use the new thalamus tool and am wondering if I need to do a full install of the latest DEV version to do so. As I am still working on certain aspects of the analyses I've run so far, I don't want to overwrite my main FS installation mid analysis. Is it possible to download the toolbox and add it to my current dev version or is it best just to do another install with teh complete new Dev version? Is it possible to run the Thalamus analysis as an addtional component without having to rerun the recon_all again? Thanks and regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Using the new Thalamus tool
External Email - Use Caution Thanks Douglas, I'll be sure to run my recon-all with the stable version and then run the rest on a second run. Thanks for the help. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: 11 September 2018 18:12:39 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using the new Thalamus tool And just to be clear, you should run only the thalamus, hippo, amyg, brainstem segmentations in dev. Do not run recon-all using the dev version. Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] On 09/11/2018 07:32 AM, Erik O'Hanlon wrote: > > External Email - Use Caution > > Thanks Eugenio, > > > I'll intall the latest dev version so. How long does it typically take > to run a subject through the thalamus pipeline typically? > > > Thanks again for the prompt reply. Very much appreciated. > > > Cheers > > > Erik > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Iglesias > Gonzalez, Eugenio > *Sent:* 10 September 2018 18:00:20 > *To:* freesurfer@nmr.mgh.harvard.edu; Freesurfer support list > *Subject:* Re: [Freesurfer] Using the new Thalamus tool > > External Email - Use Caution > > Dear Erik, > Installing only the thalamic tool is technically possible but requires > a level of hacking that i don't want to encourage or support ;-) > Please install the new dev on a separate directory, and make > FREESURFER_HOME point to that the directory (and source freesurfer) to > run the thalamic tool. No need to rerun recon-all on the subjects. > Cheers > Eugenio > > Sent from my phone, please excuse brevity and typos > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Erik O'Hanlon > > *Sent:* Thursday, September 6, 2018 3:44:57 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Using the new Thalamus tool > > External Email - Use Caution > > Hi FS Experts > > > I've run my data through the brainstem, hippocampus and amygdala > following the usual Recon_all and using the developmental version > downloaded and stalled around Jan2018. I'd like to use the new > thalamus tool and am wondering if I need to do a full install of the > latest DEV version to do so. As I am still working on certain aspects > of the analyses I've run so far, I don't want to overwrite my main FS > installation mid analysis. Is it possible to download the toolbox and > add it to my current dev version or is it best just to do another > install with teh complete new Dev version? Is it possible to run the > Thalamus analysis as an addtional component without having to rerun > the recon_all again? > > > Thanks and regards > > > Erik > > > *Erik O'Hanlon* > Postdoctoral researcher > > *RCSI* Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont D9 Ireland > *T: *8093740 > *E: *erikohan...@rcsi.ie *W: *www.rcsi.com <http://www.rcsi.com/> > > /Transforming Healthcare Education, Research and Service: RCSI > Strategic Plan 2018-2022 <http://www.rcsi.ie/strategy2018>/ > > > > > > *Erik O'Hanlon* > Postdoctoral researcher > > *RCSI* Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont D9 Ireland > *T: *8093740 > *E: *erikohan...@rcsi.ie *W: *www.rcsi.com <http://www.rcsi.com/> > > /Transforming Healthcare Education, Research and Service: RCSI > Strategic Plan 2018-2022 <http://www.rcsi.ie/strategy2018>/ > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cerikohanlon%40rcsi.ie%7C5054bee0dc7c40e204ae08d61809f843%7C607041e7a8124670bd3030f9db210f06%7C0%7C0%7C636722828434630922&sdata=XVY5uESPLfsTzpCcZTMRLFWr4S2LfaTKl8SJi16RT9U%3D&reserved=0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed
[Freesurfer] loading and rendering the Amygdala nuclei only in Freeview
External Email - Use Caution Hi FS Experts, I'm trying to make some images of my amygdala nuclei in freeview and selected my T1 as background and then loaded up lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz image which loads up perfectly. I selected the "show existing labels " and the freesurfer colour LUT but when I select the range for 7001-7015 for amygdala only, the hippocampal subfields are still there. Is there a way to only load the amygdala nuclei. I'm sure it's something simple I'm just not doing, but I can't seem to get it to work. Any pointers gladly accepted Thanks Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:AS_BRONZE_IIDD_65c26b0a-ea45-42c8-956e-5d84e884e4e6.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview
External Email - Use Caution Thanks Eugenio, I'll do that. Much appreciated. best regards Erik Postdoctoral Research Fellow Dept. Of Psychiatry Royal College of Surgeons in Ireland ERC Building Beaumont Hospital Dublin & Dept. Of Psychiatry Trinity College Institute of Neuroscience The Llyod Institute Trinity College Dublin D2 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 16 November 2018 15:45:27 To: Freesurfer support list Subject: Re: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview External Email - Use Caution Hi Erik, If you render labels >7000, you shouldn’t see a rendering of the subfields – but they will indeed remain visible in the orthogonal views. If you want to get rid of them, you can use mri_threshold: mri_threshold lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz6999 onlyAmyg.mgz Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology http://www.jeiglesias.com From: on behalf of Erik O'Hanlon Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:AS_BRONZE_IIDD_65c26b0a-ea45-42c8-956e-5d84e884e4e6.png] Reply-To: Freesurfer support list Date: Friday, 16 November 2018 at 08:15 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview External Email - Use Caution Hi FS Experts, I'm trying to make some images of my amygdala nuclei in freeview and selected my T1 as background and then loaded up lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz image which loads up perfectly. I selected the "show existing labels " and the freesurfer colour LUT but when I select the range for 7001-7015 for amygdala only, the hippocampal subfields are still there. Is there a way to only load the amygdala nuclei. I'm sure it's something simple I'm just not doing, but I can't seem to get it to work. Any pointers gladly accepted Thanks Erik Erik O'Hanlon Postdoctoral researcher [cid:image001.png@01D47D99.7BDC9930] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> RCSI Homepage - Royal College of Surgeons in Ireland<http://www.rcsi.com/> www.rcsi.com RCSI provides extensive education and training in the healthcare professions at undergraduate and postgraduate level. Learn about our undergraduate courses in medicine, pharmacy and physiotherapy, our surgical training and our range of postgraduate opportunities. Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:image002.png@01D47D99.7BDC9930] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Longitudinal processing and paralllel flag
External Email - Use Caution Hi FS experts, I'm running a longitudinal process with three time points per subject and was wondering if you can advise on the typical time to process? Can the -parallel flag be added to the base and long steps? I'm running this on a cluster that has 16 core nodes with 32gigs of ram so it might give me a good tme saving if these steps can be parallelized. Thanks and regards Erik Postdoctoral Research Fellow Dept. Of Psychiatry Royal College of Surgeons in Ireland ERC Building Beaumont Hospital Dublin & Dept. Of Psychiatry Trinity College Institute of Neuroscience The Llyod Institute Trinity College Dublin D2 Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:AS_BRONZE_IIDD_65c26b0a-ea45-42c8-956e-5d84e884e4e6.png] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] SUIT cerebellum parcellations
External Email - Use Caution Dear FS Experts, Just wondering if it's possible to use the SUIT labels in the LUT to obtain cerebellar quantification measures and also to make masks for tractography specific to each area? Thanks in advance Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cerebellum Masks
External Email - Use Caution Dear Experts, Is it possible to use the SUITS labels (#601-628) in the LUT to make masks and extract volume measures. I ultimately want to use the masks for tractography purposes. Can I use the mri_extract to pull out the specific ROI's and if so do I use it with aparc+aseg file. Any details and guidance would be very much appreciated. Thanks Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Using The Buckner Cerebellum Parcellations
External Email - Use Caution Dear FS Experts, I'd like to use the Bruckner 7 Network parcellations and have downloaded the files as per the wiki link. My Freesurfer analysis on all my subjects is sub millimetre and I have conformed my data to that using the -cm in my recon_all. I can run the recon_all with the same settings for the FSL MNI 152 1mm template as described but is there a straightforward way to get the Buckner nii file to match that space? Thanks in advance for any advice Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] longitudinal LME stats
External Email - Use Caution Dear FS experts, I have run the longitudinal pipeline on a dataset with three timepoints. I am particularly interested in the longitudinal hippocampal and amygdala data and want to run LME on these. I've made the qdec table with the id age, sex and time between scans etc. and have exported all the hippocamapal and amygdala volumes to csv files to merge with demographic data. Should I smooth the hippocampal and amygdala measures before running the LME? Do I run Qcache and if so do I use recon-all -long SubID_tp1 subIDbase -qcache In the LME wiki instructions it gives an example for the mass-univariate approach on thickness. Is the study_average referring to the fsaverage ? Should I be using the ICV from the cross-sectional runs or the ICV measures in the "long" folders which refer? Thanks and any help is very much appreciated. Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampal subfields
External Email - Use Caution Dear FS experts, I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to extract the amygdala and the head body tail subfields bui I'm wondering how to extract the regular FS60 volume measures? I have the three versions (FS60, HBT and CA mgz files in my long mri directories but I just keep getting the HBT volumes. I tried quantifyHAsubregions.sh hippoSf T1.long Outputfilename and that gives me the HBT measures What command do I use to pull out the FS60 subfield measures from my long mri directories? Thanks for any help. Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfields
External Email - Use Caution Hi Eugenio So I ran the new Amygdala and hippocampus tool on my longitudinal data and from that I got the three output files as described on the wiki( the FS60, HBT and the CA) which these mgz files are in the long mri directories for each subject. This all looks fine. The issue is that I want to look at the FS 60 version of the subfields and export these rather than the HBT versions. When I use the script to extract all the measures to a file, it works fine and I have the amygdala volumes but for the hippocampus, I get the HBT versions. How do you get the extract script to output the FS60 subfield measures? Is it possible? If not can I simply add the HBT sections for each subfield to equate to the FS 60 measures? Thanks for your prompt reply. Much appreciated Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Sent: Friday 27 August 2021 22:02 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields Dear Erik I’m not sure I understand. What does your output file look like? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1lOExJeky8AFqkFfrzJ79hMnVWS5jkY1XvPoEM7_fiDyZiO2NCivnLmj1kLuPRm2w88EDcWDJFNg74iZ5sXiGABC3n_oKlQ0uGC_9nPN9HjPWymVUYBrBeTboJSI7XzVHe1kg37ir15P16T7suVpnbFAkPhobCBTQwqWnq4d9hmBt5I1ybk3_w9_yFktbjWWuVl6uJ_6k6IUCsPgYNWjI5LqC-dobHYl3W_y6GhIsiANkJk6bKdBmRwDZDkB7o8lLevPO3On0jPYRQRhL13Rhgg/http%3A%2F%2Fwww.jeiglesias.com On Aug 27, 2021, at 16:14, Erik O'Hanlon mailto:ohanl...@tcd.ie>> wrote: External Email - Use Caution External Email - Use Caution Dear FS experts, I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to extract the amygdala and the head body tail subfields bui I'm wondering how to extract the regular FS60 volume measures? I have the three versions (FS60, HBT and CA mgz files in my long mri directories but I just keep getting the HBT volumes. I tried quantifyHAsubregions.sh hippoSf T1.long Outputfilename and that gives me the HBT measures What command do I use to pull out the FS60 subfield measures from my long mri directories? Thanks for any help. Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1KpjtWxWHIKAUquh4Uydr2e7YoRAgRF-HVDiv4BqhdUa-0X_RYf1Li44OPUb4fzHZIku_uP_nDzEHktcAlacLIl1hd9lb-vboaoyuevb--4OLvVJY8D-2mPUnYe5D5GgDInCvdRE3Et0ssZlwAYhNcjF7xV5ai2-gfZsXCKvmgILBMTAYKq_kgkrwxrLkJO2m7J2YKio6TFWV8TzwLVcr0BEUu8Y5f47aoybkO5V35ewmCWkmvIfk42BpyRVAx1O7T5J_-G7rtK7GW2osJ8Ho7Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfields
External Email - Use Caution Hi Eugenio, Thanks so much for you reply. I will do that so. Just by way understanding the outputs I have , so the extract script only pulls the HBT automatically, and you need to simply add these together for the FS60 measures ? You can't modify the extract tool to read the FS60 data automatically? Thanks again for your help. I will follow your instructions. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Sent: Monday 30 August 2021 11:05 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields Oh, now I understand. Yeah you can add the head, body and tail segments of each subfield to get 6.0 type of measurements ;-) Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1knFRpDOFuoCvGaipHjXiJ2cPhPsiPMOeHi81MNBHC1pYD-xRCQzIgqWb6hExpRNqTqerIYAq3W6EUbKPQIYN6loykvYK69agvpqiJpixFB0HZxJ3tLZE5VfSe-gO2GqcRvGhQHCfYZw4IhoipbJUOi9v0tL5ajYH_Hv7r1WXRikWcSkenidoPo0bU8j8yPC21LqHlMB6c51XU6vq9XyKWHpExMjlIdUrOvuDxTOVyvXXGX6Z6Vom55EXxKNHs5XA4SgCapcbUOZufvnpzZ1tIw/http%3A%2F%2Fwww.jeiglesias.com On Aug 28, 2021, at 08:20, Erik O'Hanlon mailto:ohanl...@tcd.ie>> wrote: External Email - Use Caution External Email - Use Caution Hi Eugenio So I ran the new Amygdala and hippocampus tool on my longitudinal data and from that I got the three output files as described on the wiki( the FS60, HBT and the CA) which these mgz files are in the long mri directories for each subject. This all looks fine. The issue is that I want to look at the FS 60 version of the subfields and export these rather than the HBT versions. When I use the script to extract all the measures to a file, it works fine and I have the amygdala volumes but for the hippocampus, I get the HBT versions. How do you get the extract script to output the FS60 subfield measures? Is it possible? If not can I simply add the HBT sections for each subfield to equate to the FS 60 measures? Thanks for your prompt reply. Much appreciated Erik From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> Sent: Friday 27 August 2021 22:02 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Hippocampal subfields Dear Erik I’m not sure I understand. What does your output file look like? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1knFRpDOFuoCvGaipHjXiJ2cPhPsiPMOeHi81MNBHC1pYD-xRCQzIgqWb6hExpRNqTqerIYAq3W6EUbKPQIYN6loykvYK69agvpqiJpixFB0HZxJ3tLZE5VfSe-gO2GqcRvGhQHCfYZw4IhoipbJUOi9v0tL5ajYH_Hv7r1WXRikWcSkenidoPo0bU8j8yPC21LqHlMB6c51XU6vq9XyKWHpExMjlIdUrOvuDxTOVyvXXGX6Z6Vom55EXxKNHs5XA4SgCapcbUOZufvnpzZ1tIw/http%3A%2F%2Fwww.jeiglesias.com<http://secure-web.cisco.com/1lOExJeky8AFqkFfrzJ79hMnVWS5jkY1XvPoEM7_fiDyZiO2NCivnLmj1kLuPRm2w88EDcWDJFNg74iZ5sXiGABC3n_oKlQ0uGC_9nPN9HjPWymVUYBrBeTboJSI7XzVHe1kg37ir15P16T7suVpnbFAkPhobCBTQwqWnq4d9hmBt5I1ybk3_w9_yFktbjWWuVl6uJ_6k6IUCsPgYNWjI5LqC-dobHYl3W_y6GhIsiANkJk6bKdBmRwDZDkB7o8lLevPO3On0jPYRQRhL13Rhgg/http%3A%2F%2Fwww.jeiglesias.com> On Aug 27, 2021, at 16:14, Erik O'Hanlon mailto:ohanl...@tcd.ie>> wrote: External Email - Use Caution External Email - Use Caution Dear FS experts, I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to extract the amygdala and the head body tail subfields bui I'm wondering how to extract the regular FS60 volume measures? I have the three versions (FS60, HBT and CA mgz files in my long mri directories but I just keep getting the HBT volumes. I tried quantifyHAsubregions.sh hippoSf T1.long Outputfilename and that gives me the HBT measures What command do I use to pull out the FS60 subfield measures from my long mri directories? Thanks for any help. Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1KpjtWxWHIKAUquh4Uydr2e7YoRAgRF-HVDiv4BqhdUa-0X_RYf1Li44OPUb4fzHZIku_uP_nDzEHktcAlacLIl1hd9lb-vboaoyuevb--4OLvVJY8D-2mPUnYe5D5GgDInCvdRE3Et0ssZlwAYhNcjF7xV5ai2-gfZsXCKvmgILBMTAYKq_kgkrwxrLkJO2m7J2YKio6TFWV8TzwLVcr0BEUu8Y5f47aoybkO5V35ewmCWkmvIfk42BpyRVAx1O7T5J_-G7rtK7GW2osJ8Ho7Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.
[Freesurfer] Brainstem segmentation
External Email - Use Caution Dear Experts, We hope to acquire some multishell dwi and structural data to investigate tracts passing through the Locus Coeruleus (LC) and we want to apply the brainstem segmentation to our structural data to obtain subject specific LC masks. Is it possible to feed multispectral data into the brainstem segmentation ? Is it possible to acquire a high res volume capturing the LC in greater detail and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in the delineation of the LC roi and quantification of the LC volume? If it's possible to use an additional small volume like this, do I need to pre-process it using recon-all and what is the optimal way to co-register the small volume to the whole brain T1 to assist in the mask generation? Any guidance is very much appreciated. Best regards and thanks, Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Brainstem segmentation
External Email - Use Caution Dear Eugenio, Thanks so much for your reply. I will certainly follow your instructions on "small volume" registration. That will certainly allow us to benefit from the more specialized volume showing neuromelanin within the LC area in conjunction with the whole brain T1 and brainstem component. Very much appreciated Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Sent: Thursday 23 September 2021 03:27 To: Freesurfer support list Subject: Re: [Freesurfer] Brainstem segmentation Dear Erik, I never put together a multi-spectral version of the brainstem segmentation because, given the coarse structures that we segment (midbrain, pons, medulla, scp), there’s pretty much nothing to be gained from additional contrasts. In terms of registration: if your “small volume” is acquired during the same session as the 1mm T1 you’ve processed with FreeSurfer, they should be almost overlapping in RAS coordinates. You can then use mri_robust_register with the —noinit flag to register the volumes. I would strongly encourage you to use the small volume as target of the registration and the 1mm T1 as source; you can always invert the resulting rigid transform matrix to go in the other direction. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1utF6ii16FKVLSJtWVYU_QqP1mwtxTj9C4VzTH0TRLK0acGF8EMLbdFaa8Dv_159f-HS2e-xguAL8vJmmD2VOC4slo1o-a6ZCZtFDMcEKgC_T_QAMj73Xew1zhJund5MNGcWTs7ADio9g4zzJv7DZXaAzNPvwJo2QHoo6c-L5tKD9r9TYrOvElG4-wm585jaBTDh_iuTOL60mLjxf-tjaC2Y7ZyRSgjEQyYnzMYJhAZw1Y70cho9-SxLgPeWpesRGZp0h4bUwIoOGTfjh-YarDA/http%3A%2F%2Fwww.jeiglesias.com On Sep 20, 2021, at 18:43, Erik O'Hanlon mailto:ohanl...@tcd.ie>> wrote: External Email - Use Caution External Email - Use Caution Dear Experts, We hope to acquire some multishell dwi and structural data to investigate tracts passing through the Locus Coeruleus (LC) and we want to apply the brainstem segmentation to our structural data to obtain subject specific LC masks. Is it possible to feed multispectral data into the brainstem segmentation ? Is it possible to acquire a high res volume capturing the LC in greater detail and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in the delineation of the LC roi and quantification of the LC volume? If it's possible to use an additional small volume like this, do I need to pre-process it using recon-all and what is the optimal way to co-register the small volume to the whole brain T1 to assist in the mask generation? Any guidance is very much appreciated. Best regards and thanks, Erik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1e0K0Qpt0HADjYKHLwxppb4VSEbFeiC_dzSdIRHl2SDVei2h5UnWj-3vTHhN3pQNH5dTWqo-lu63OpinjMFQT0UUQlI8CHL3PRPCbDoyAEpNMabaTXXe6RgREyKlF8obA7SpvgXD1KpOMw5_jP2A_ZIoPdNyW5Np--AZuEet24QMc0-7gcoxz-3G3wwdy2tmLYMK2gd65icEt_cJkFdIdS8Uow2kUYcrAi7WrOEt3Cn2Vg07g3nO09LK0Jv2Y8MX9VTG0wXPDt9CfmqSfnUrdXw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
