Re: [Freesurfer] vertex-wise covariate for gyrification index
That's fine. mri_glmfit-sim has a little anxiety when it finds mri_glmfit options it does not recognize. doug On 1/26/15 5:00 PM, angela.fav...@unipd.it wrote: > Hi Doug, > thank you for this hint. > I have included --pvr in my mri_glmfit command using a stack of cortical > thickness maps of the same hemisphere (and same subjects in the same > order). I also added a column in my design matrix. It seems to work. Only > when I use the mri_glmfit-sim command, this message appears: > > WARNING: unrecognized mri_glmfit cmd option --pvr > > WARNING: unrecognized mri_glmfit cmd option /qdec/lh_LGI_vtw/thick.mgh > > but everything seems to work anyway (and clusters of differences do not > disappear!!). > Is it all correct? > > Thank you for your help! > > Angela > > >> QDEC does not allow it, but you can do it with mri_glmfit with the --pvr >> option. Run mri_glmfit with --help to get more info. >> doug >> >> On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote: >>> Hi all, >>> I wrote a paper about gyrification in a sample of malnourished patients. >>> I >>> found only little overlap between maps of significantly rediced cortical >>> thickness and maps of significantly reduced gyrification index (in >>> comparison to a group of healthy controls). >>> One of the reviewer raised the question that this is not sufficient to >>> demonstrate that reduced gyrification is not due to reduced cortical >>> thickness (or GM volume) and suggest to perform a between group analysis >>> using cortical thickness (or volume) maps as vertex-wise covariates. >>> Is it possible to perform this type of analysis? I believe that QDEC >>> does >>> not allow it >>> >>> Thank you >>> >>> Angela >>> >>> >>> >>> >>> Hi Maria it's really hard to say - you'll need to try it out. There aren't strong prior constraints on skull shape, but if the shape of the brain is too different, things may degrade Bruce On Fri, 23 Jan 2015, Maria Holland wrote: > Hi all, > I am starting a project analyzing patients with cranial deformities. > How > robust is the automatic cortical reconstruction process - i.e., would > it > be > able to handle deformed skulls? Similar to this picture: > > http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis > .png > > I am also wondering about the possibility of getting information about > the > intermediate steps of the local gyrification calculation. Like, could > we > get information on the pial and outer pial surface paths on each > individual > slice, before that information is turned into a 3D surface? > > Thanks for your help! > > ~ Maria > > ___ 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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] vertex-wise covariate for gyrification index
Hi Doug, thank you for this hint. I have included --pvr in my mri_glmfit command using a stack of cortical thickness maps of the same hemisphere (and same subjects in the same order). I also added a column in my design matrix. It seems to work. Only when I use the mri_glmfit-sim command, this message appears: WARNING: unrecognized mri_glmfit cmd option --pvr WARNING: unrecognized mri_glmfit cmd option /qdec/lh_LGI_vtw/thick.mgh but everything seems to work anyway (and clusters of differences do not disappear!!). Is it all correct? Thank you for your help! Angela > QDEC does not allow it, but you can do it with mri_glmfit with the --pvr > option. Run mri_glmfit with --help to get more info. > doug > > On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote: >> Hi all, >> I wrote a paper about gyrification in a sample of malnourished patients. >> I >> found only little overlap between maps of significantly rediced cortical >> thickness and maps of significantly reduced gyrification index (in >> comparison to a group of healthy controls). >> One of the reviewer raised the question that this is not sufficient to >> demonstrate that reduced gyrification is not due to reduced cortical >> thickness (or GM volume) and suggest to perform a between group analysis >> using cortical thickness (or volume) maps as vertex-wise covariates. >> Is it possible to perform this type of analysis? I believe that QDEC >> does >> not allow it >> >> Thank you >> >> Angela >> >> >> >> >> >>> Hi Maria >>> >>> it's really hard to say - you'll need to try it out. There aren't >>> strong >>> prior constraints on skull shape, but if the shape of the brain is too >>> different, things may degrade >>> >>> Bruce >>> >>> >>> On Fri, 23 Jan 2015, Maria Holland wrote: >>> Hi all, I am starting a project analyzing patients with cranial deformities. How robust is the automatic cortical reconstruction process - i.e., would it be able to handle deformed skulls? Similar to this picture: http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis .png I am also wondering about the possibility of getting information about the intermediate steps of the local gyrification calculation. Like, could we get information on the pial and outer pial surface paths on each individual slice, before that information is turned into a 3D surface? Thanks for your help! ~ Maria ___ >>> 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
Re: [Freesurfer] vertex-wise covariate for gyrification index
QDEC does not allow it, but you can do it with mri_glmfit with the --pvr option. Run mri_glmfit with --help to get more info. doug On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote: > Hi all, > I wrote a paper about gyrification in a sample of malnourished patients. I > found only little overlap between maps of significantly rediced cortical > thickness and maps of significantly reduced gyrification index (in > comparison to a group of healthy controls). > One of the reviewer raised the question that this is not sufficient to > demonstrate that reduced gyrification is not due to reduced cortical > thickness (or GM volume) and suggest to perform a between group analysis > using cortical thickness (or volume) maps as vertex-wise covariates. > Is it possible to perform this type of analysis? I believe that QDEC does > not allow it > > Thank you > > Angela > > > > > >> Hi Maria >> >> it's really hard to say - you'll need to try it out. There aren't strong >> prior constraints on skull shape, but if the shape of the brain is too >> different, things may degrade >> >> Bruce >> >> >> On Fri, 23 Jan 2015, Maria Holland wrote: >> >>> Hi all, >>> I am starting a project analyzing patients with cranial deformities. >>> How >>> robust is the automatic cortical reconstruction process - i.e., would it >>> be >>> able to handle deformed skulls? Similar to this picture: >>> >>> http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis >>> .png >>> >>> I am also wondering about the possibility of getting information about >>> the >>> intermediate steps of the local gyrification calculation. Like, could >>> we >>> get information on the pial and outer pial surface paths on each >>> individual >>> slice, before that information is turned into a 3D surface? >>> >>> Thanks for your help! >>> >>> ~ Maria >>> >>> ___ >> 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
