Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate
My apologies Doug... I thought that this email had all the history...
Narly, sorry for "invading" your discussion...
My questions came from the first email of Narly which referred to the bug in mris_preproc:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19821.html
This bug also exist in FS 5.0, right? I'm using 5.0 and until now I've used aparcstats2table to get Brodmann Area measures (CT and surface area of the thresholded labels) and total CT and surface area of each hemisphere. Does the bug also affect these measures or it is fine to use them?
Now I want to run a whole-brain analysis with qdec but to do so I'll have to run qcache with 5.3 which already has the bug fixed, correct? Is qcache equivalent to mris_preproc?
Hope I was more clear this time...
Thank you, Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Sorry, the thread of the email that explains the problem and the fix are not included below. Can you re-explain? We get a lot of emails here and it is not possible to remember the context of each one. doug
On 03/18/2014 11:32 AM, _andreia_@sapo.pt wrote:
Hi all,
just two quick questions: to what FS version is this related? And what is wrong to do if one does not have the fix? Using what stats/procedures?
Thanks, Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
why would one control for total brain volume in doing vertex-based
analyses when the vertex-based measures are computed in standard space?
The vertex-based measures are computed in individual space, not standard space doug
On 03/17/2014 05:12 PM, Narly Golestani wrote:
Dear Doug,
Many thanks for your answers.
- The bug was related to how the measures were converted to standard
space - I?d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses).
This question has nothing to do with the bug. People generally use ICV or total brain volume when exploring cortical volume or surface area, but it is inappropriate for thicknss studies doug
Regarding the last point (which indeed has nothing to do with the bug, sorry for having given the impression that I thought that it did), why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? I realize that this has to be done for ROI analyses since these measures are in native space.
Thanks again, and best, Narly.
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Have you checked the release notes?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
On 03/19/2014 01:57 PM, _andreia_@sapo.pt wrote:
My apologies Doug... I thought that this email had all the history...
Narly, sorry for "invading" your discussion...
My questions came from the first email of Narly which referred to the bug in mris_preproc:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19821.html
This bug also exist in FS 5.0, right? I'm using 5.0 and until now I've used aparcstats2table to get Brodmann Area measures (CT and surface area of the thresholded labels) and total CT and surface area of each hemisphere. Does the bug also affect these measures or it is fine to use them?
Now I want to run a whole-brain analysis with qdec but to do so I'll have to run qcache with 5.3 which already has the bug fixed, correct? Is qcache equivalent to mris_preproc?
Hope I was more clear this time...
Thank you, Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Sorry, the thread of the email that explains the problem and the fix are not included below. Can you re-explain? We get a lot of emails here and it is not possible to remember the context of each one. doug
On 03/18/2014 11:32 AM, _andreia_@sapo.pt wrote:
Hi all,
just two quick questions: to what FS version is this related? And what is wrong to do if one does not have the fix? Using what stats/procedures?
Thanks, Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
why would one control for total brain volume in doing vertex-based
analyses when the vertex-based measures are computed in standard space?
The vertex-based measures are computed in individual space, not standard space doug
On 03/17/2014 05:12 PM, Narly Golestani wrote:
Dear Doug,
Many thanks for your answers.
- The bug was related to how the measures were converted to
standard space - I?d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses).
This question has nothing to do with the bug. People generally use ICV or total brain volume when exploring cortical volume or surface area, but it is inappropriate for thicknss studies doug
Regarding the last point (which indeed has nothing to do with the bug, sorry for having given the impression that I thought that it did), why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? I realize that this has to be done for ROI analyses since these measures are in native space.
Thanks again, and best, Narly.
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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_andreia_＠sapo.pt -
Douglas N Greve