Dear Freesurfer Experts,
In qdec for question: "Does the average thickness differ between X and Y" we received blue colored regions, meaning that thickness for group Y is lower then X ?
We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats.
in results: for each ROI, mean cortical thickness of Y group are higher then X.
is it a mistake, or the question was misunderstood ?
Sincerely, Alex.
blue means that X>Y. So that sounds like it is compatible with your ROI results, yes? doug
Alex Hanganu wrote:
Dear Freesurfer Experts,
In qdec for question: "Does the average thickness differ between X and Y" we received blue colored regions, meaning that thickness for group Y is lower then X ?
We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats.
in results: for each ROI, mean cortical thickness of Y group are higher then X.
is it a mistake, or the question was misunderstood ?
Sincerely, Alex.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
right, qdec shows healthy (X) > patients (Y)
mris_anatomical_stats show: Y > X
but I didn't do mri_surf2surf, I just copied the ROI.label in every subjects /label/ directory.
Thank you for your help Doug !
Have a great day,
Alex.
--- En date de : Ven 25.2.11, Douglas N Greve greve@nmr.mgh.harvard.edu a écrit :
De: Douglas N Greve greve@nmr.mgh.harvard.edu Objet: Re: [Freesurfer] Qdec - ROI - different thickness results À: "Alex Hanganu" hanganu.alexandru@yahoo.de Cc: "FS Mailing List" Freesurfer@nmr.mgh.harvard.edu Date: Vendredi 25 février 2011, 16h52
blue means that X>Y. So that sounds like it is compatible with your ROI results, yes? doug
Alex Hanganu wrote:
Dear Freesurfer Experts,
In qdec for question: "Does the average thickness differ between X and Y" we received blue colored regions, meaning that thickness for group Y is lower then X ?
We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats.
in results: for each ROI, mean cortical thickness of Y group are higher then X.
is it a mistake, or the question was misunderstood ?
Sincerely, Alex.
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
sorry, I should have said mri_label2label, not mri_surf2surf doug
Alex Hanganu wrote:
right, qdec shows healthy (X) > patients (Y)
mris_anatomical_stats show: Y > X
but I didn't do mri_surf2surf, I just copied the ROI.label in every subjects /label/ directory.
Thank you for your help Doug !
Have a great day,
Alex.
--- En date de : *Ven 25.2.11, Douglas N Greve /greve@nmr.mgh.harvard.edu/* a écrit :
De: Douglas N Greve <greve@nmr.mgh.harvard.edu> Objet: Re: [Freesurfer] Qdec - ROI - different thickness results À: "Alex Hanganu" <hanganu.alexandru@yahoo.de> Cc: "FS Mailing List" <Freesurfer@nmr.mgh.harvard.edu> Date: Vendredi 25 février 2011, 16h52 blue means that X>Y. So that sounds like it is compatible with your ROI results, yes? doug Alex Hanganu wrote: > Dear Freesurfer Experts, > > In qdec for question: > "Does the average thickness differ between X and Y" > we received blue colored regions, meaning that thickness for group Y is lower then X ? > > We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats. > > in results: for each ROI, mean cortical thickness of Y group are higher then X. > > is it a mistake, or the question was misunderstood ? > > Sincerely, > Alex. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu </mc/compose?to=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 </mc/compose?to=greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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.
Thank You Doug !
We created a specific label for each subject using cmd>
mri_label2label --srcsubject fsaverage --srclabel (the ROI.label created in qdec) --trgsubject SUBJECT_NAME --trglabel $SUBJECTS_DIR/SUBJECT_NAME/label/ROIx-lh.label --regmethod surface --hemi lh
after that> mris_anatomical_stats -l (ROIx-lh.label address) -b SUBJECT_NAME lh
the results are the same, qdec: X>Y mris: X<Y
Did we miss another step again ?
Sincerely, Alex.
--- En date de : Ven 25.2.11, Douglas N Greve greve@nmr.mgh.harvard.edu a écrit :
De: Douglas N Greve greve@nmr.mgh.harvard.edu Objet: Re: [Freesurfer] Qdec - ROI - different thickness results À: "Alex Hanganu" hanganu.alexandru@yahoo.de Cc: "FS Mailing List" Freesurfer@nmr.mgh.harvard.edu Date: Vendredi 25 février 2011, 17h12
sorry, I should have said mri_label2label, not mri_surf2surf doug
Alex Hanganu wrote:
right, qdec shows healthy (X) > patients (Y)
mris_anatomical_stats show: Y > X
but I didn't do mri_surf2surf, I just copied the ROI.label in every subjects /label/ directory.
Thank you for your help Doug !
Have a great day,
Alex.
--- En date de : *Ven 25.2.11, Douglas N Greve /greve@nmr.mgh.harvard.edu/* a écrit :
De: Douglas N Greve greve@nmr.mgh.harvard.edu Objet: Re: [Freesurfer] Qdec - ROI - different thickness results À: "Alex Hanganu" hanganu.alexandru@yahoo.de Cc: "FS Mailing List" Freesurfer@nmr.mgh.harvard.edu Date: Vendredi 25 février 2011, 16h52
blue means that X>Y. So that sounds like it is compatible with your ROI results, yes? doug
Alex Hanganu wrote: > Dear Freesurfer Experts, > > In qdec for question: > "Does the average thickness differ between X and Y" > we received blue colored regions, meaning that thickness for group Y is lower then X ? > > We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats. > > in results: for each ROI, mean cortical thickness of Y group are higher then X. > > is it a mistake, or the question was misunderstood ? > > Sincerely, > Alex. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu /mc/compose?to=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 /mc/compose?to=greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
the easiest way to determine X from Y and blue from red (ie, which group is getting thicker or thinner) is to Ctrl-right click on a vertex within the region of interest on the cortex result display. a plot will appear showing the raw thickness values for your groups, and which-is-which should obvious.
n.
On Fri, 2011-02-25 at 15:33 +0000, Alex Hanganu wrote:
Dear Freesurfer Experts,
In qdec for question: "Does the average thickness differ between X and Y" we received blue colored regions, meaning that thickness for group Y is lower then X ?
We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats.
in results: for each ROI, mean cortical thickness of Y group are higher then X.
is it a mistake, or the question was misunderstood ?
Sincerely, Alex.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much for the idea Nick, this explained everything. In qdec red means X>Y
we didn't notice the thickness data on that plot at first :(
Have a wonderful week !
Sincerely, Alex.
--- En date de : Dim 27.2.11, Nick Schmansky nicks@nmr.mgh.harvard.edu a écrit :
De: Nick Schmansky nicks@nmr.mgh.harvard.edu Objet: Re: [Freesurfer] Qdec - ROI - different thickness results À: "Alex Hanganu" hanganu.alexandru@yahoo.de Cc: "FS Mailing List" Freesurfer@nmr.mgh.harvard.edu Date: Dimanche 27 février 2011, 0h28
the easiest way to determine X from Y and blue from red (ie, which group is getting thicker or thinner) is to Ctrl-right click on a vertex within the region of interest on the cortex result display. a plot will appear showing the raw thickness values for your groups, and which-is-which should obvious.
n.
On Fri, 2011-02-25 at 15:33 +0000, Alex Hanganu wrote:
Dear Freesurfer Experts,
In qdec for question: "Does the average thickness differ between X and Y" we received blue colored regions, meaning that thickness for group Y is lower then X ?
We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats.
in results: for each ROI, mean cortical thickness of Y group are higher then X.
is it a mistake, or the question was misunderstood ?
Sincerely, Alex.
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@nmr.mgh.harvard.edu
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Alex Hanganu -
Douglas N Greve -
Nick Schmansky