[Freesurfer] Fwd: F-test with mkcontrast
I would be grateful if someone could answer my question below from some time ago. Dear all, I need to specify this matrix as my F contrast [1 -1 0; 0 1 -1] , however I'm not sure how I can do this. Usually for a matrix like [1 0 0; 0 1 0] i use mkcontrast-sess -analysis analysis-name -contrast ftest -a 1 -a 2 -nosumconds I can use -c for -1 in the contrast, but using nosumconds, will assume that -a and -c are from different contrasts, so this does not work apparently -a 1 -c 2 -a 2 -c 3 -nosumconds because each a and c are assumed to be from different vectors, not from one vector. I'd appreciate if anyone could help me. Best wishes, James ___ 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: Re: ERROR: matrix is ill-conditioned or badly scaled
Hi both, Problem is solved. Apparently there were commas in the FSGD which caused covariates to be erroneous. Thanks, regards, Sander -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Sanne Oostermeijer Verzonden: donderdag 7 mei 2015 10:02 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: Re: ERROR: matrix is ill-conditioned or badly scaled Hi Doug, I did. The email below is another FS user having the same error. Sander, I had the same problem due to having only 1 female in one of the groups (and correcting for gender). -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N Greve Verzonden: woensdag 6 mei 2015 17:47 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: Re: ERROR: matrix is ill-conditioned or badly scaled did you see the email I sent last night about you having one group with only one subject? On 05/06/2015 08:50 AM, Verfaillie, Sander wrote: Dear Douglasor colleague, Currently I am working on one of the last steps of freesurfer analyses; the mri_glmdir. However, trying multiple FSGD versions and after reading several posts one this topic on your Harvard webpage, the ill-conditioned or badly scaled message keeps on popping up. I have checked the number of lines, column spacing. Furthermore I have used excel2.txt conversion for creating the FSGD file, which in previous analyses worked out perfectly fine. Command line: mri_glmfit --y rh.age_gender_scanner_FU_time.00.mgh --fsgd FSGD_v4_2.fsgd dods --C Contrast_test.mtx --surf fsaverage lh --cortex --glmdir rh.FSGD_v4_2_4covariates.glmdir After visual inspection of the Xg.dat file it seems columns are slightly shifted. I am not sure whether this causes the error. rh.FSGD_v4_2_4covariates.glmdir/Xg.dat Could you help me out? I have attached the necessary files. Sample size: n=305, 2 class, 4 covariates The aim of this analyses is to look at contrast group1group2 while regressing out the effects of gender, scanner type, age and follow-up time. A second aim is to look at an interaction between FU_time and group1group2. Thanks a lot in advance, kind regards, Sander Verfaillie Drs. S.C.J. Verfaillie Neuropsycholoog - Onderzoeker VU Medical CenterDepartment of Neurology, Alzheimer Center Department of Radiology Nuclear Medicine De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands Tel: +31 20 4448527 Room: PK -1 Z 039 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. Dit e-mailbericht is alleen bestemd voor de geadresseerde(n). Het kan informatie bevatten die persoonlijk is en niet openbaar mag worden gemaakt krachtens wet- of regelgeving. Gebruik door anderen is niet toegestaan. Indien u niet de geadresseerde(n) bent, wordt u verzocht de verzender hiervan op de hoogte te stellen en het bericht te verwijderen ___ 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] DTI tensor estimation
Dear freesurfer experts, I looked at the help text for the dt_recon function, and wonder how the GLM is setup for the DTI data, is there a paper that describes how freesurfer does it? Specifically, I'm interested in how a dataset with 3-4 different b-values is analyzed. Is there a dummy variable in the GLM that models the different b-values, since the data from different b-values have very different variance? http://freesurfer.net/fswiki/dt_recon Regards, Anders ___ 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 erikohan...@rcsi.ie 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 again, FS6 is not out yet, but hopefully soon. The instructions for the new hippocampal subfield module are here: http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields 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 erikohan...@rcsi.ie To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 3:36:21 PM 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 erikohan...@rcsi.ie 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. ___ 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 erikohan...@rcsi.ie 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 once more, there is no specific longitudinal subfield module, BUT you can run the subfield code on the longitudinally processed subjects (i.e., those with tpNid.long.templateid added to their name). 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 erikohan...@rcsi.ie To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 3:42:26 PM Subject: 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 erikohan...@rcsi.ie 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Exporting the Hippocampus
Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ 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] Exporting the Hippocampus
I am currently using the files: posterior_Left-Hippocampus.nii posterior_Right-Hippocampus.nii (I converted to the nifti format to use the load_nifti matlab function). Thanks, Chester On May 8, 2015, at 1:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: do you mean the hippocampus in aseg.mgz or the hippocampal subfields? On 05/08/2015 01:26 PM, Chester Dolph wrote: Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- BEGIN-ANTISPAM-VOTING-LINKS -- NOTE: This message was trained as non-spam. If this is wrong, please correct the training as soon as possible. Teach CanIt if this mail (ID 03Optt94s) is spam: Spam: https://www.spamtrap.odu.edu/canit/b.php?i=03Optt94sm=664b1eae3462t=20150508c=s Not spam: https://www.spamtrap.odu.edu/canit/b.php?i=03Optt94sm=664b1eae3462t=20150508c=n Forget vote: https://www.spamtrap.odu.edu/canit/b.php?i=03Optt94sm=664b1eae3462t=20150508c=f -- END-ANTISPAM-VOTING-LINKS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Exporting the Hippocampus
do you mean the hippocampus in aseg.mgz or the hippocampal subfields? On 05/08/2015 01:26 PM, Chester Dolph wrote: Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Fwd: F-test with mkcontrast
This actually can't be done in version 5.3. An alternative is to make two t-contrasts then merge them together like this mri_concat analysis/con1/sig.nii.gz analysis/con2/sig.nii.gz --max-bonfcor --o sig12.nii.gz doug On 05/08/2015 02:03 AM, james pardon wrote: I would be grateful if someone could answer my question below from some time ago. |Dear all,| | | |I need to specify this matrix as my F contrast [1 -1 0; 0 1 -1] , however I'm not sure how I can do this. Usually for a matrix like [1 0 0; 0 1 0] i use| |mkcontrast-sess -analysis analysis-name -contrast ftest -a 1 -a 2 -nosumconds| |I can use -c for -1 in the contrast, but using nosumconds, will assume that -a and -c are from different contrasts, so this does not work apparently| | | |-a 1 -c 2 -a 2 -c 3 -nosumconds| |because each a and c are assumed to be from different vectors, not from one vector. I'd appreciate if anyone could help me.| | | |Best wishes,| |James| ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] DTI tensor estimation
It is standard dti analysis, so it computes the log(y), then sets up a seven column matrix with 1 b*gx*gx b*gx*gy b*gx*gz b*gy*gy b*gy*gz b*gz*gz The b, gx, gy, and gz change with each row according to the bval and bvec files doug On 05/08/2015 05:29 AM, Anders Eklund wrote: Dear freesurfer experts, I looked at the help text for the dt_recon function, and wonder how the GLM is setup for the DTI data, is there a paper that describes how freesurfer does it? Specifically, I'm interested in how a dataset with 3-4 different b-values is analyzed. Is there a dummy variable in the GLM that models the different b-values, since the data from different b-values have very different variance? http://freesurfer.net/fswiki/dt_recon Regards, Anders ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Exporting the Hippocampus
In the last post I meant “using: Would the correct way of extracting the intensities using the segmentation look something like this? I would like to use raw intensity values of a ROI for texture analysis. I would prefer to have all of the extracted ROI in the same coordinate space so comparisons may be made between MRI scans. By “extract”, I mean isolate the ROI and ignore all other volumes. On May 8, 2015, at 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: when you say extract what do you mean exactly? On 05/08/2015 02:36 PM, Chester Dolph wrote: So I looked up the aseg file and the taliarch.label_intensities.txt. Would the correct way of extracting the intensities from the segmentation look something like this? if( aseg.mgz voxel == my taliarch label intensity of interest (e.g., Right_hippocampus values 1.49 0.0 94) my extracted mri voxel = brain.mgz voxel else my extracted mri voxel = 0 end (if there’s a nice script or command that does this, please let me know). Thanks, Chester On May 8, 2015, at 1:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: do you mean the hippocampus in aseg.mgz or the hippocampal subfields? On 05/08/2015 01:26 PM, Chester Dolph wrote: Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- BEGIN-ANTISPAM-VOTING-LINKS -- Teach CanIt if this mail (ID 01OpuTnR3) is spam: Spam: https://www.spamtrap.odu.edu/canit/b.php?i=01OpuTnR3m=cd20831f56b5t=20150508c=s Not spam: https://www.spamtrap.odu.edu/canit/b.php?i=01OpuTnR3m=cd20831f56b5t=20150508c=n Forget vote: https://www.spamtrap.odu.edu/canit/b.php?i=01OpuTnR3m=cd20831f56b5t=20150508c=f -- END-ANTISPAM-VOTING-LINKS ___ Freesurfer mailing list
Re: [Freesurfer] DTI tensor estimation
Yes, but the signal can have rather different variance due to the different b-values. So it would make sense to use a heteroscedastic GLM, where the variance is allowed to change over the samples. In the more conventional homoscedastic GLM, the variance is assumed to be constant over time / samples. Is this ignored in freesurfer, or is it solved by using weighted least squares? - Anders Från: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] f#246;r Douglas N Greve [gr...@nmr.mgh.harvard.edu] Skickat: den 8 maj 2015 19:40 Till: freesurfer@nmr.mgh.harvard.edu Ämne: Re: [Freesurfer] DTI tensor estimation It is standard dti analysis, so it computes the log(y), then sets up a seven column matrix with 1 b*gx*gx b*gx*gy b*gx*gz b*gy*gy b*gy*gz b*gz*gz The b, gx, gy, and gz change with each row according to the bval and bvec files doug On 05/08/2015 05:29 AM, Anders Eklund wrote: Dear freesurfer experts, I looked at the help text for the dt_recon function, and wonder how the GLM is setup for the DTI data, is there a paper that describes how freesurfer does it? Specifically, I'm interested in how a dataset with 3-4 different b-values is analyzed. Is there a dummy variable in the GLM that models the different b-values, since the data from different b-values have very different variance? http://freesurfer.net/fswiki/dt_recon Regards, Anders ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Exporting the Hippocampus
You can use mri_binarize with the match option to get a mask of hippocampus from aseg.mgz (use 17 or left hippo and 53 for right, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then use mri_mask to mask the norm.mgz to get a volume of the intensities doug On 05/08/2015 03:11 PM, Chester Dolph wrote: In the last post I meant “using: Would the correct way of extracting the intensities using the segmentation look something like this? I would like to use raw intensity values of a ROI for texture analysis. I would prefer to have all of the extracted ROI in the same coordinate space so comparisons may be made between MRI scans. By “extract”, I mean isolate the ROI and ignore all other volumes. On May 8, 2015, at 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: when you say extract what do you mean exactly? On 05/08/2015 02:36 PM, Chester Dolph wrote: So I looked up the aseg file and the taliarch.label_intensities.txt. Would the correct way of extracting the intensities from the segmentation look something like this? if( aseg.mgz voxel == my taliarch label intensity of interest (e.g., Right_hippocampus values 1.49 0.0 94) my extracted mri voxel = brain.mgz voxel else my extracted mri voxel = 0 end (if there’s a nice script or command that does this, please let me know). Thanks, Chester On May 8, 2015, at 1:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: do you mean the hippocampus in aseg.mgz or the hippocampal subfields? On 05/08/2015 01:26 PM, Chester Dolph wrote: Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- BEGIN-ANTISPAM-VOTING-LINKS -- Teach CanIt if this mail (ID 01OpuTnR3) is spam: Spam: https://www.spamtrap.odu.edu/canit/b.php?i=01OpuTnR3m=cd20831f56b5t=20150508c=s Not spam: https://www.spamtrap.odu.edu/canit/b.php?i=01OpuTnR3m=cd20831f56b5t=20150508c=n Forget
Re: [Freesurfer] hippocampal subfields
Erik, I haven't tried, but I'm pretty certain that you can use v5.3 results. I'm not aware of any dependency built-in to the v6 stream that the new hippocampal-subfields stream uses. Nick On Fri, 2015-05-08 at 18:10 +, Erik O'Hanlon wrote: 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 erikohan...@rcsi.ie 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] DTI tensor estimation
Why is the noise greater with greater bvalue? In any case, it just uses ordinary LS, so assume homoscedastic. On 05/08/2015 01:54 PM, Anders Eklund wrote: Yes, but the signal can have rather different variance due to the different b-values. So it would make sense to use a heteroscedastic GLM, where the variance is allowed to change over the samples. In the more conventional homoscedastic GLM, the variance is assumed to be constant over time / samples. Is this ignored in freesurfer, or is it solved by using weighted least squares? - Anders Från: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] f#246;r Douglas N Greve [gr...@nmr.mgh.harvard.edu] Skickat: den 8 maj 2015 19:40 Till: freesurfer@nmr.mgh.harvard.edu Ämne: Re: [Freesurfer] DTI tensor estimation It is standard dti analysis, so it computes the log(y), then sets up a seven column matrix with 1 b*gx*gx b*gx*gy b*gx*gz b*gy*gy b*gy*gz b*gz*gz The b, gx, gy, and gz change with each row according to the bval and bvec files doug On 05/08/2015 05:29 AM, Anders Eklund wrote: Dear freesurfer experts, I looked at the help text for the dt_recon function, and wonder how the GLM is setup for the DTI data, is there a paper that describes how freesurfer does it? Specifically, I'm interested in how a dataset with 3-4 different b-values is analyzed. Is there a dummy variable in the GLM that models the different b-values, since the data from different b-values have very different variance? http://freesurfer.net/fswiki/dt_recon Regards, Anders ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] VOI's from Sabuncu et al. 2012
Aaron, The are the *.oasis.chubs.* labels found in the $FREESURFER_HOME/subjects/fsaverage/labels directory. You will need to use mris_label2label to map them to your subject. Have a look at the 'ba labels' section of recon-all for an example of this mapping operation. N. On Thu, 2015-05-07 at 18:49 +, Aaron Goldman wrote: Hello, I had a question about Sabuncu et al. 2012 (http://cercor.oxfordjournals.org/content/22/11/2653.long), in which the authors generated a series of ROIs related to incipient Alzheimer's disease: Based on the resulting statistical maps, we delineated seven regions of interest (ROIs) on the average cortical surface template that demonstrated the greatest magnitude of bilateral cortical thinning in incipient AD participants relative to older controls. These regions include the entorhinal cortex, temporopolar cortex, lateral temporal cortex, inferior parietal cortex, inferior parietal sulcus, posterior cingulate cortex, and inferior frontal cortex. These ROIs and corresponding statistical maps have been published elsewhere (Sabuncu et al. 2011) and are made publicly available with FreeSurfer. Specifically, I was wondering what the phrase made publicly available with FreeSurfer meant. Does this mean I can find the ROI's if I look in a subject's label folder, or that there's some command I can run to generate the ROI's? Thanks, Aaron ___ 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
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 erikohan...@rcsi.ie 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
Re: [Freesurfer] Exporting the Hippocampus
Thanks! On May 8, 2015, at 3:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can use mri_binarize with the match option to get a mask of hippocampus from aseg.mgz (use 17 or left hippo and 53 for right, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then use mri_mask to mask the norm.mgz to get a volume of the intensities doug On 05/08/2015 03:11 PM, Chester Dolph wrote: In the last post I meant “using: Would the correct way of extracting the intensities using the segmentation look something like this? I would like to use raw intensity values of a ROI for texture analysis. I would prefer to have all of the extracted ROI in the same coordinate space so comparisons may be made between MRI scans. By “extract”, I mean isolate the ROI and ignore all other volumes. On May 8, 2015, at 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: when you say extract what do you mean exactly? On 05/08/2015 02:36 PM, Chester Dolph wrote: So I looked up the aseg file and the taliarch.label_intensities.txt. Would the correct way of extracting the intensities from the segmentation look something like this? if( aseg.mgz voxel == my taliarch label intensity of interest (e.g., Right_hippocampus values 1.49 0.0 94) my extracted mri voxel = brain.mgz voxel else my extracted mri voxel = 0 end (if there’s a nice script or command that does this, please let me know). Thanks, Chester On May 8, 2015, at 1:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: do you mean the hippocampus in aseg.mgz or the hippocampal subfields? On 05/08/2015 01:26 PM, Chester Dolph wrote: Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.
Re: [Freesurfer] tracking edits
Deirdre, the -show-edits flag in recon-all will print edits. N. On Thu, 2015-05-07 at 12:29 -0400, Deirdre O Shea wrote: Dear Freesurfer experts, I wondered how I might be able to track all the edits I make on each subject e.g., how many control points etc. But most specifically if there was a way to see how much ,numerically, the image has changed with manual correction following the initial FreeSurfer run. Thanks in advance, Deirdre ___ 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] recon-all compared to dev table
Kody, The ReconAllDevTable wiki page describes the stream that is under development. For v5.3, you will want this page: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3 Be aware though that the commands listed may not be *exactly* as that found in a v5.3 run, as this table is manually created and abbreviated for readability. But if you find discrepancies with a v5.3 run of yours, feel free to email me or the list pointing out the mistakes, so that we can update it. I've also updated the main wiki page so that people are not directed to the ReconAllDevTable page. Side note, if you want try our 'dev' version (documented by ReconAllDevTable), which will become v6 in a few weeks, you can get it here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ and would appreciate testing feedback, as we'd hate to release v6 with some dumb mistake that we didn't catch in testing. Nick On Thu, 2015-05-07 at 11:51 -0700, zal...@u.washington.edu wrote: Dear freesurfer team, I'm very new to freesurfer, and I am currently working my way through the recon-all dev table functions (listed here: http://freesurfer.net/fswiki/ReconAllDevTable) step-by-step in preparation for processing a large amount of participant volumetric data. While doing so I've noticed some inconsistencies between the dev table and the series of functions called by the recon-all command. For example: -The apas2aseg function listed in the dev table does not exist in my bin file (nor does it appear to be called by recon-all). -The cortical ribbon output occurs after the three cortical parcellation steps/creation of the anatomical.stats files (instead of prior to these steps like the dev table suggests) -The MNI intensity correction (the mri_nu_correct.mni function) is not called following the skull-stripping. I downloaded the latest version of freesurfer (5.3.0) last week so it should be up-to-date. Thank you for taking the time to answer my questions, -Kody J. Zalewski ___ 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] Interaction contrast setup
what are you trying to test an interaction between? Can you send the first lines of your fsgd file? On 05/07/2015 10:41 AM, Sarah Banducci wrote: Hi all- I have been trying to determine the most appropriate way to set up an interaction contrast for glmfit. For my purposes I'm interested in looking at the interaction two performance variables while covarying demographics. I have 2 classes set to male and female and the first columns in my fsgd file are demeaned age and education. I have found 3 ways people suggest setting up an interaction contrast: 1- Putting the contrast in one row: 0 0 0 0 -.5 -.5 .5 .5 2- Using two rows for the contrast: 0 0 0 0 .5 .5 0 0 0 0 0 0 0 0 .5 .5 3- Creating an actual interaction term where the values are multiplied together in a new column of the fsgd file 0 0 0 0 0 0 0 0 .5 .5 I would be grateful to know how people set up this contrast. Also I would like to know how you run it (positive or negative) and subsequently how you interpret the results. Thanks, Sarah Banducci ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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.ieW: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 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 erikohan...@rcsi.ie 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.
