Hi Donna, the whole purpose of showing Screenshot-Map Functional Volumes To Surfaces.png is to show that every other steps are the same, except this, so I did select map to spec with atlas .
Since the bug you saw in SPM5 atlas for left SPM5, there is only 1 coordinate, that's why I couldn't use them as they are not comparable with the right hemisphere. I only compared SPM5 right hemisphere with Flirt and MRITOTAL, the difference was really minimal and both look good. Do you think I can go ahead use FLIRT space and spec or MRITOTAL, seems their space are essentially the same according to one of your comments in Caret forum, and indeed there is little discrepancy when I compared them with the ones I projected onto the right hemisphere SPM5. Thank you again! Best, On Thu, Apr 14, 2011 at 9:57 AM, Donna Dierker <[email protected]>wrote: > The only thing that seems amiss here is this capture: > > Screenshot-Map Functional Volumes To Surfaces.png > > You should see something more like what you see for the right hem. > > The only explanation I can come up with is that you selected Map to Spec > File, rather than Map to Spec File with Atlas. Because this capture is > certainly consistent with the former, but not the latter. > > On 04/13/2011 02:39 PM, Xiaozhen You wrote: > > Interesting..my caret version is caretV5.615 > > I do use Map to > > Spec File With Atlas, and select SPM5 for Space, and see this option: > > > > PALS_B12 Multi-Fid Map LEFT hemisphere (73730 nodes), SPM5 space > > but without both AFM and MFM checkboxes. > > I'm attaching the screenshots to see the differences between the GUI > > when I select for left and right. Hope you can open them. > > > > Thank you again! > > Best, > > Xiaozhen > > > > On Wed, Apr 13, 2011 at 3:29 PM, Donna Dierker > > <[email protected] <mailto:[email protected]>> wrote: > > > > You might have an incomplete Caret distribution. When you press > > Map to > > Spec File With Atlas, and select SPM5 for Space, you should see > > this option: > > > > PALS_B12 Multi-Fid Map LEFT hemisphere (73730 nodes), SPM5 space > > > > ... with both AFM and MFM checkboxes. > > > > Are you perhaps not pressing Map to Spec File With Atlas? If not, > try > > doing so. > > > > On 04/13/2011 02:14 PM, Xiaozhen You wrote: > > > Thank you Donna! > > > I now get good mapping on right hemisphere, as it provides AFM and > > > MFM, however, the corresponding left hemisphere atlas file for SPM5 > > > space always only have 1 coordinate files, and it doesn't give > > me AFM > > > and MFM, seems it only gives AFM, which is just not showing the > > > clusters that I can see in MFM. No matter which spec file I opened > > > right now, somehow mapping to SPM5 left and right atlas would > > give me > > > different available coordinates (which is fine as I can open new > > coord > > > after the mapping is done), but the metric seems only allow me to > > > write one (MFM) for left atlas.. > > > > > > Sorry for keep on asking you all these questions, hopefully this > > is it! :) > > > Thanks! > > > Best, > > > Xiaozhen > > > > > > On Wed, Apr 13, 2011 at 12:48 PM, Donna Dierker > > > <[email protected] <mailto:[email protected]> > > <mailto:[email protected] > > <mailto:[email protected]>>> wrote: > > > > > > Go here: > > > > > > > > > http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 > > < > http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 > > > > > > > < > http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 > > < > http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 > >> > > > > > > Download the zip file. Extract it. > > > > > > Use this spec file: > > > > > > PALS_B12.RIGHT.STANDARD-SCENES.73730.spec > > > > > > It doesn't have the SPM5 fiducial in it, but you can load that > > > directly > > > by opening the spec file and using File: Open Data file: and > > > navigating > > > to the Caret distribution directory, > > > > > > data_files/fmri_mapping_files/Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM5.clean.73730.coord. > > > > > > Map to the PALS SPM5 Right atlas only, and see if you get > better > > > results. > > > > > > Donna > > > > > > On 04/13/2011 09:54 AM, Xiaozhen You wrote: > > > > Hi Donna, > > > > Is there a way I can find the specific right hemishpere atlas > > > (instead > > > > of both hemisphere) for SPM5 space? > > > > Thank you! > > > > Best, > > > > > > > > > > > > On Tue, Apr 12, 2011 at 6:00 PM, Xiaozhen You > > > <[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>> > > > > <mailto:[email protected] > > <mailto:[email protected]> <mailto:[email protected] > > <mailto:[email protected]>>>> > > > wrote: > > > > > > > > Sorry to hear that you are sick Donna. and thank you for > > > replying > > > > promptly! > > > > The problem is I was using SPM8 to normalize my data > > into their > > > > EPI template, and the spec i found recommended by > > caret was > > > > "the > > > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec" or > > > > MGH group was > > > > " > > PALS.B12.BOTH-HEMS.For-Stereotaxic-foci-analyses.73730.spec". > > > > For both I tried, and the space I chose SPM5, as there > > is no > > > SPM8. > > > > But weirdly, for atlas under SPM5, there is only left > > > > human.pals.multi.fidmap.Left.hemisphere.73730, but no > > > > corresponding > > human.pals.multi.fidmap.right.hemisphere.73730... > > > > > > > > Do you think the choices I made were reasonable, and > > do you know > > > > where I can find the right hemisphere atlas for SPM5 that > > > > associate with a specific spec file good for fmri mapping > > > using SPM8? > > > > > > > > Thank you again and hope you feel better! > > > > Best, > > > > > > > > On Tue, Apr 12, 2011 at 5:38 PM, Donna Dierker > > > > <[email protected] > > <mailto:[email protected]> <mailto:[email protected] > > <mailto:[email protected]>> > > > <mailto:[email protected] > > <mailto:[email protected]> > > > <mailto:[email protected] > > <mailto:[email protected]>>>> wrote: > > > > > > > > I am at home sick today, so it's not easy for me to > > > replicate > > > > your results. > > > > > > > > But when I have trouble like this, I revert to > > using single > > > > hem spec files > > > > -- RIGHT or LEFT. Map only to one or the other. Do > > > them one > > > > at a time. > > > > See if it helps. > > > > > > > > > Dear Caret experts, > > > > > I've been using Caret to map the connectivity > > results, and > > > > just notice > > > > > that > > > > > the patterns always look the same on both > > hemisphere, even > > > > when I know > > > > > there > > > > > is no DLPFC on the left hemisphere but only on > right > > > > hemisphere, (which is > > > > > validated by overlaying them on MRICron, but it > > just look > > > > the same on > > > > > CARET! > > > > > Here is what I did: > > > > > 1. generate NIFTI format filr for thresholded > > spmT.hdr > > > file > > > > > 2. menu-attribute- map volume to > > surface-metric(function) > > > > surface > > > > > data->add > > > > > volumes from disk->map spec file with > > atlas->choose " > > > > PALS.B12.*BOTH*-* > > > > > HEMS.For-*Stereotaxic-foci-analyses.73730.spec", > > space " > > > > SPM5" (as I > > > > > processed everything in SPM8), atlas " > > > > > > > > > > > > > > > PALS.B12.*BOTH*-*HEMS.For-*Stereotaxic-foci-analyses.73730.spec".->enclosing > > > > > voxel. > > > > > 3. view results, I loaded the metric and spec file, > > > primary > > > > overlay > > > > > ("metric"), then model I chose > > > > > > > > > > > > > > > "fiducial.human.pals_B12.Left.Average.B1-12.fiducial_moritotal_clean.73730.coord". > > > > > Then change the model to > > > > > > > > > > > > > > > "fiducial.human.pals_B12.right.Average.B1-12.fiducial_moritotal_clean.73730.coord". > > > > > > > > > > They look the same, even with different metric > > setting ( > > > > like threshold > > > > > selection) > > > > > Could you help me figure out what did I do wrong? > > > Thank you! > > > > > Best, > > > > > > > > > > -- > > > > > Xiaozhen You, PhD > > > > > Developmental Cognitive Neuroscience Lab > > > > > Georgetown University > > > > > 401 White-Gravenor > > > > > 3700 O Street, NW > > > > > Washington DC 20057 > > > > > [email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>> > > > <mailto:[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>>> > > > > > 202-687-9133 <tel:202-687-9133> > > <tel:202-687-9133 <tel:202-687-9133>> <tel:202-687-9133 > > <tel:202-687-9133> > > > <tel:202-687-9133 <tel:202-687-9133>>>/ > > > > > 202-687-8223 <tel:202-687-8223> > > <tel:202-687-8223 <tel:202-687-8223>> <tel:202-687-8223 > > <tel:202-687-8223> > > > <tel:202-687-8223 <tel:202-687-8223>>> > > > > > _______________________________________________ > > > > > caret-users mailing list > > > > > [email protected] > > <mailto:[email protected]> > > > <mailto:[email protected] > > <mailto:[email protected]>> > > > > <mailto:[email protected] > > <mailto:[email protected]> > > > <mailto:[email protected] > > <mailto:[email protected]>>> > > > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > > _______________________________________________ > > > > caret-users mailing list > > > > [email protected] > > <mailto:[email protected]> > > > <mailto:[email protected] > > <mailto:[email protected]>> > > > > <mailto:[email protected] > > <mailto:[email protected]> > > > <mailto:[email protected] > > <mailto:[email protected]>>> > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > > > > > > > > > -- > > > > Xiaozhen You, PhD > > > > Developmental Cognitive Neuroscience Lab > > > > Georgetown University > > > > 401 White-Gravenor > > > > 3700 O Street, NW > > > > Washington DC 20057 > > > > [email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>> > > > <mailto:[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>>> > > > > 202-687-9133 <tel:202-687-9133> <tel:202-687-9133 > > <tel:202-687-9133>> <tel:202-687-9133 <tel:202-687-9133> > > > <tel:202-687-9133 <tel:202-687-9133>>>/ > > > > 202-687-8223 <tel:202-687-8223> <tel:202-687-8223 > > <tel:202-687-8223>> <tel:202-687-8223 <tel:202-687-8223> > > > <tel:202-687-8223 <tel:202-687-8223>>> > > > > > > > > > > > > > > > > > > > > -- > > > > Xiaozhen You, PhD > > > > Developmental Cognitive Neuroscience Lab > > > > Georgetown University > > > > 401 White-Gravenor > > > > 3700 O Street, NW > > > > Washington DC 20057 > > > > [email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>> > > > <mailto:[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>>> > > > > 202-687-9133 <tel:202-687-9133> <tel:202-687-9133 > > <tel:202-687-9133>>/ > > > > 202-687-8223 <tel:202-687-8223> <tel:202-687-8223 > > <tel:202-687-8223>> > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > > caret-users mailing list > > > > [email protected] > > <mailto:[email protected]> > > > <mailto:[email protected] > > <mailto:[email protected]>> > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > _______________________________________________ > > > caret-users mailing list > > > [email protected] > > <mailto:[email protected]> > > <mailto:[email protected] > > <mailto:[email protected]>> > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > > > > -- > > > Xiaozhen You, PhD > > > Developmental Cognitive Neuroscience Lab > > > Georgetown University > > > 401 White-Gravenor > > > 3700 O Street, NW > > > Washington DC 20057 > > > [email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>> > > > 202-687-9133 <tel:202-687-9133>/ > > > 202-687-8223 <tel:202-687-8223> > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > caret-users mailing list > > > [email protected] > > <mailto:[email protected]> > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] <mailto: > [email protected]> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > -- > > Xiaozhen You, PhD > > Developmental Cognitive Neuroscience Lab > > Georgetown University > > 401 White-Gravenor > > 3700 O Street, NW > > Washington DC 20057 > > [email protected] <mailto:[email protected]> > > 202-687-9133/ > > 202-687-8223 > > > > ------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > -- Xiaozhen You, PhD Developmental Cognitive Neuroscience Lab Georgetown University 401 White-Gravenor 3700 O Street, NW Washington DC 20057 [email protected] 202-687-9133/ 202-687-8223
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