[Freesurfer] Subject: Re: Zero cortical thickness
Hi Douglas, I meant a surface area extracted from a surface based atlas. Thanks Adonay ___ 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] Subject: Re: Zero cortical thickness
Hi I looked at the distribution areas with almost zero thickness and when I saw they were on one hemisphere, I checked my bash script and found out that for the left cortex it was calling the right hemisphere areas. However, I still have a few subjects which have zero thickness in some areas of my parcelled atlas. This zero thickness is it caused by a segmentation or a sphere reconstruction error/imperfection (in which case the value should be NaN), or is it capturing a brain structural characteristic worth to account for? Thanks Adonay On Mon, Aug 15, 2016 at 3:06 PM, A Nunes wrote: > Hi Douglas, > > I meant a surface area extracted from a surface based atlas. > > Thanks > Adonay ___ 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] Subject: Re: Zero cortical thickness
please include previous correspondence. Do you mean the area of a vertex or the area of an ROI? On 08/15/2016 06:06 PM, A Nunes wrote: > Hi Douglas, > > I meant a surface area extracted from a surface based atlas. > > Thanks > Adonay > ___ > 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] Subject: Re: Zero cortical thickness
I mean the area of an ROI On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve wrote: > please include previous correspondence. Do you mean the area of a vertex > or the area of an ROI? > > On 08/15/2016 06:06 PM, A Nunes wrote: >> Hi Douglas, >> >> I meant a surface area extracted from a surface based atlas. >> >> Thanks >> Adonay >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> Hi I looked at the distribution areas with almost zero thickness and when I saw they were on one hemisphere, I checked my bash script and found out that for the left cortex it was calling the right hemisphere areas. However, I still have a few subjects which have zero thickness in some areas of my parcelled atlas. This zero thickness is it caused by a segmentation or a sphere reconstruction error/imperfection (in which case the value should be NaN), or is it capturing a brain structural characteristic worth to account for? Thanks Adonay Date: Mon, 15 Aug 2016 16:27:24 -0400 From: Douglas Greve Subject: Re: [Freesurfer] Zero cortical thickness To: freesurfer@nmr.mgh.harvard.edu Message-ID: <8c1593aa-77fc-333e-e7d7-1901f9a39...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed what do you mean by "area"? do you mean one of the cortical ROIs or do you mean a general location? On 8/15/16 4:13 PM, A Nunes wrote: > Hi, > > I have read in the mailing list about zero cortical thickness, but I > still have some doubts. > > I am calculating the average cortical thickness of some areas, and > there are a few that almost all the subjects' thickness is zero, > others only some subjects score zero. For the ones that almost all > subjects is zero, I would guess is not considered cortical, however, > all my areas are cortical. > > - If I compute a ttest against two groups, should I set the zeros as > NaNs? or are the zero thickness meaningful (a genuine measure or a > segmentation artifact)? > > -Should I use the -l ?h.cortex.label to avoid having zero thickness in > some areas? If so, at which point? the commands used are: > > mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h > --sval-annot fsaverage/label/?h.areas.annot --tval > $SUBJECTS_DIR/subjid/label/?h.areas.annot > > mris_anatomical_stats -a > $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot > -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b subjid ?h > > > Thanks > Adonay > ___ > 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] Subject: Re: Zero cortical thickness
which ROIs are coming up zero? Have you looked at the area maps for that subject for that ROI? On 08/16/2016 01:16 PM, A Nunes wrote: > I mean the area of an ROI > > On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve > wrote: >> please include previous correspondence. Do you mean the area of a vertex >> or the area of an ROI? >> >> On 08/15/2016 06:06 PM, A Nunes wrote: >>> Hi Douglas, >>> >>> I meant a surface area extracted from a surface based atlas. >>> >>> Thanks >>> Adonay >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> > Hi > > I looked at the distribution areas with almost zero thickness and when > I saw they were on one hemisphere, I checked my bash script and found > out that for the left cortex it was calling the right hemisphere > areas. > However, I still have a few subjects which have zero thickness in some > areas of my parcelled atlas. This zero thickness is it caused by a > segmentation or a sphere reconstruction error/imperfection (in which > case the value should be NaN), or is it capturing a brain structural > characteristic worth to account for? > > Thanks > Adonay > Date: Mon, 15 Aug 2016 16:27:24 -0400 > From: Douglas Greve > Subject: Re: [Freesurfer] Zero cortical thickness > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <8c1593aa-77fc-333e-e7d7-1901f9a39...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > what do you mean by "area"? do you mean one of the cortical ROIs or do > you mean a general location? > > > On 8/15/16 4:13 PM, A Nunes wrote: >> Hi, >> >> I have read in the mailing list about zero cortical thickness, but I >> still have some doubts. >> >> I am calculating the average cortical thickness of some areas, and >> there are a few that almost all the subjects' thickness is zero, >> others only some subjects score zero. For the ones that almost all >> subjects is zero, I would guess is not considered cortical, however, >> all my areas are cortical. >> >> - If I compute a ttest against two groups, should I set the zeros as >> NaNs? or are the zero thickness meaningful (a genuine measure or a >> segmentation artifact)? >> >> -Should I use the -l ?h.cortex.label to avoid having zero thickness in >> some areas? If so, at which point? the commands used are: >> >> mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h >> --sval-annot fsaverage/label/?h.areas.annot --tval >> $SUBJECTS_DIR/subjid/label/?h.areas.annot >> >> mris_anatomical_stats -a >> $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot >>-f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b subjid ?h >> >> >> Thanks >> Adonay >> ___ >> 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. 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.
