you are welcome. if labelling is your ultimate goal, you may find that rather than using caret to make paint volumes, you might try using the data here
scalablebrainatlas.incf.org you need to use matlab to get these images, stack them and reconstruct them into a 3d nifti from a file of bytes (miconv is handy for that). that way you get an index of names also. I've got code for that but it's 2 or 3 years old. generally scalablebrainatlas is very good to explore. Same people as cocomac (except for kotter sadly) The MNI labels as distributed might be a bit frustrating. transforming caret paint data will destroy the label indexing because the header will not be preserved. try scalablebrainatlas it's really good. best, Colin On 9 July 2013 11:16, <[email protected]> wrote: > Send caret-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: Slow processing of manual error correction (Donna Dierker) > 2. Re: f99 to MNI 7 rhesus (Pablo Barttfeld) > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Mon, 8 Jul 2013 13:31:08 -0500 > Subject: Re: [caret-users] Slow processing of manual error correction > Hi Nicky, > > Sorry I can't help. I doubt there are many Windows users who edit > segmentations out there. (Could be wrong.) > > The only suggestion I have is that if you have some other program (e.g., > MRIcron) that can edit voxels, you can do your editing there; save the > resulting NIFTI volume; and then load it as a segmentation volume in Caret > and prepare for flattening as usual. > > Donna > > > On Jul 5, 2013, at 9:45 AM, Nicky Daniels <[email protected]> > wrote: > > > YOUR NAME > > > > Nicky Daniels > > > > YOUR EMAIL ADDRESS > > > > [email protected] > > > > NAME OF PROGRAM (caret5 or caret_command) > > > > Caret5 > > > > VERSION AND DATE (at top of main window in caret5 or run caret_command > without any parameters) > > > > Version 5.61 NOV13 2008 > > > > OPERATING SYSTEM (Mac/Windows/Linux) AND VERSION (Mac: Apple Menu->About > this Mac) (Linux: Run "uname -a" in a terminal window) (Windows: Start > Menu->Control Panel->System or Start Menu->Control Panel->Performance and > Maintenance->System) > > > > Windows 7 Professional 64-bit > > > > SUMMARY OF PROBLEM > > > > The process of segmentation to flattening doesn’t run smoothly on my > computer. > > > > HOW TO REPRODUCE PROBLEM; WHAT HAPPENS > > > > After segmentation, I press the D/C button to show the > Segment_ErrorCorrect overlay. When I try to edit voxels (via the pull-down > menu Volume > Segmentation > Edit Vovels) by clicking on the image, there > is a long delay (about 10sec) between the click and a voxel turning on/off. > It is ok when I click one time, but when I click several times or swipe > then the delay is noticeable. When I open a new window and put node > identify symbols on the Fiducial to locate handles etc., it takes the > program takes a long time (about 15sec) to direct to the location. > > > > WHAT SHOULD HAPPEN > > > > I am a new user, but my colleagues who assist me in the usage of caret > say that the program works remarkably slower than when they used it a year > ago on their computers. One of my colleagues is using caret to redo some of > her images and says this new version works slower as well. That is why I > tried to use older versions (5.61 and 5.51) as well, but this still didn’t > improve the speed. > > > > > > Thank you in advance for your time. > > > > Best wishes, > > Nicky > > > > ------------------------------------- > > > > Nicky Daniels > > University of Leuven (KU Leuven) > > Laboratory of Biological Psychology > > Tiensestraat 102 > > B-3000 Leuven, Belgium > > > > Email: [email protected] > > Tel.: 0163 25613 > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ---------- Forwarded message ---------- > From: Pablo Barttfeld <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Tue, 9 Jul 2013 11:08:02 +0200 > Subject: Re: [caret-users] f99 to MNI 7 rhesus > Hi Colin, thanks a lot! > Best > Pablo > > > > 2013/7/8 Colin Reveley <[email protected]> > >> What you should do is: >> >> extract F99 from the skull. extract the MNI atlas from the skull. >> >> alternatively, you might get good results by putting both the MNI and >> F99 image into ACPC and cropping them so that the non-brain material is >> nearly the same. but you might not. >> >> it's best to brain extract them. I can give you this if you need it. >> I'm not sure where by extracted MNI is but I do have one. >> >> applying SUSAN noise reduction to F99 is a good idea. >> >> you can then apply registration software to F99. And you can apply >> transforms to caret paint volumes that you've made by using caret's >> function to make paint volumes from paint columns. It is not perfect to the >> actual cortical thickness of course but you can play with the parameters. >> >> I doubt linear registration is going to do the trick. >> >> You might find that using fnirt is quite hard and slow. >> >> You might ask the mni people. >> >> You might try this. This will work. This is ours actually. you will >> need an NVIDIA GPU that is less than 3 years old and is meant for science >> or intensive computer games. >> >> http://www.bss.phy.cam.ac.uk/~ag492/ezys/ >> >> I never did manage to get the mni labelling to be of actual use. maybe >> that has changed. >> >> but you can put paint data from caret into mni like this. >> >> good luck. Let me know if I can help. I've done a lot of this. >> >> you can generate the equvalent of the attached images. >> >> actually it would be interesting to compare the paxinos labels on MNI >> made this way, and made the way they did it. >> >> with perseverance you can do more less anything you need. Our software >> does help, if you have the appropriate hardware. >> >> you could also try to make a surface from the MNI data (so downsample >> to 0.5mm). you will need to pre-process it a lot with FAST or nu_correct or >> both. it might not work. >> >> then you can try surface registration methods. >> >> best, >> >> Colin >> >> >> On 8 July 2013 18:00, <[email protected]> wrote: >> >>> Send caret-users mailing list submissions to >>> [email protected] >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> or, via email, send a message with subject or body 'help' to >>> [email protected] >>> >>> You can reach the person managing the list at >>> [email protected] >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of caret-users digest..." >>> >>> Today's Topics: >>> >>> 1. F99 to MNI (Pablo Barttfeld) >>> 2. Re: F99 to MNI (Donna Dierker) >>> 3. Re: F99 to MNI (Matt Glasser) >>> 4. Re: F99 to MNI (Pablo Barttfeld) >>> 5. Re: F99 to MNI (Donna Dierker) >>> >>> >>> ---------- Forwarded message ---------- >>> From: Pablo Barttfeld <[email protected]> >>> To: <[email protected]> >>> Cc: >>> Date: Mon, 8 Jul 2013 11:37:35 +0200 >>> Subject: [caret-users] F99 to MNI >>> Hi all, >>> I would like to map the regions in F99 into MNI space, is there a >>> function in Caret to do that? >>> Best >>> Pablo >>> >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: Donna Dierker <[email protected]> >>> To: "Caret, SureFit, and SuMS software users" < >>> [email protected]> >>> Cc: >>> Date: Mon, 8 Jul 2013 08:54:25 -0500 >>> Subject: Re: [caret-users] F99 to MNI >>> I'm pretty sure you're the first person to ask that question. Or at >>> least the first I've heard it. >>> >>> Obviously the macaque and human brains have different scales, but it >>> might, in principle, be possible. Computing a volumetric transform from >>> the F99 individual monkey volume to either MNI305 or avg152T1 mean human >>> atlases doesn't seem likely to work well. >>> >>> But I think David registered the F99 surface to the same 73730 mesh as >>> the PALS human atlas. (He had a good reason for doing so.) If that is in >>> the Sept 2006 tutorial dataset, then you could load the F99 paint areas on >>> the PALS atlas and use Attributes: Paint to project them from surface-land >>> to volume-land, using the PALS flirt, SPM, or MRITOTAL surface as the >>> mapping substrate. >>> >>> Hopefully David will chime in if the F99-to-PALS correspondence makes >>> this a bad idea. >>> >>> (Let's face it: We must always approach cross-species registration with >>> a long list of caveats.) >>> >>> >>> On Jul 8, 2013, at 4:37 AM, Pablo Barttfeld <[email protected]> >>> wrote: >>> >>> > Hi all, >>> > I would like to map the regions in F99 into MNI space, is there a >>> function in Caret to do that? >>> > Best >>> > Pablo >>> > >>> > >>> > _______________________________________________ >>> > caret-users mailing list >>> > [email protected] >>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: Matt Glasser <[email protected]> >>> To: "Caret, SureFit, and SuMS software users" < >>> [email protected]> >>> Cc: >>> Date: Mon, 8 Jul 2013 09:53:44 -0500 >>> Subject: Re: [caret-users] F99 to MNI >>> I cannot imagine being able to do this well with volumetric registration. >>> >>> Matt. >>> >>> On 7/8/13 8:54 AM, "Donna Dierker" <[email protected]> wrote: >>> >>> >I'm pretty sure you're the first person to ask that question. Or at >>> >least the first I've heard it. >>> > >>> >Obviously the macaque and human brains have different scales, but it >>> >might, in principle, be possible. Computing a volumetric transform from >>> >the F99 individual monkey volume to either MNI305 or avg152T1 mean human >>> >atlases doesn't seem likely to work well. >>> > >>> >But I think David registered the F99 surface to the same 73730 mesh as >>> >the PALS human atlas. (He had a good reason for doing so.) If that is >>> >in the Sept 2006 tutorial dataset, then you could load the F99 paint >>> >areas on the PALS atlas and use Attributes: Paint to project them from >>> >surface-land to volume-land, using the PALS flirt, SPM, or MRITOTAL >>> >surface as the mapping substrate. >>> > >>> >Hopefully David will chime in if the F99-to-PALS correspondence makes >>> >this a bad idea. >>> > >>> >(Let's face it: We must always approach cross-species registration with >>> >a long list of caveats.) >>> > >>> > >>> >On Jul 8, 2013, at 4:37 AM, Pablo Barttfeld <[email protected]> >>> >wrote: >>> > >>> >> Hi all, >>> >> I would like to map the regions in F99 into MNI space, is there a >>> >>function in Caret to do that? >>> >> Best >>> >> Pablo >>> >> >>> >> >>> >> _______________________________________________ >>> >> 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 >>> >>> >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: Pablo Barttfeld <[email protected]> >>> To: "Caret, SureFit, and SuMS software users" < >>> [email protected]> >>> Cc: >>> Date: Mon, 8 Jul 2013 16:01:55 +0200 >>> Subject: Re: [caret-users] F99 to MNI >>> Hi Donna, thanks for your response. >>> Sorry I was not clear enough, I meant the macaque MNI space, not the >>> human MNI. >>> thanks a lot >>> Pablo >>> >>> >>> 2013/7/8 Donna Dierker <[email protected]> >>> >>>> I'm pretty sure you're the first person to ask that question. Or at >>>> least the first I've heard it. >>>> >>>> Obviously the macaque and human brains have different scales, but it >>>> might, in principle, be possible. Computing a volumetric transform from >>>> the F99 individual monkey volume to either MNI305 or avg152T1 mean human >>>> atlases doesn't seem likely to work well. >>>> >>>> But I think David registered the F99 surface to the same 73730 mesh as >>>> the PALS human atlas. (He had a good reason for doing so.) If that is in >>>> the Sept 2006 tutorial dataset, then you could load the F99 paint areas on >>>> the PALS atlas and use Attributes: Paint to project them from surface-land >>>> to volume-land, using the PALS flirt, SPM, or MRITOTAL surface as the >>>> mapping substrate. >>>> >>>> Hopefully David will chime in if the F99-to-PALS correspondence makes >>>> this a bad idea. >>>> >>>> (Let's face it: We must always approach cross-species registration >>>> with a long list of caveats.) >>>> >>>> >>>> On Jul 8, 2013, at 4:37 AM, Pablo Barttfeld <[email protected]> >>>> wrote: >>>> >>>> > Hi all, >>>> > I would like to map the regions in F99 into MNI space, is there a >>>> function in Caret to do that? >>>> > Best >>>> > Pablo >>>> > >>>> > >>>> > _______________________________________________ >>>> > 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 >>>> >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: Donna Dierker <[email protected]> >>> To: "Caret, SureFit, and SuMS software users" < >>> [email protected]> >>> Cc: >>> Date: Mon, 8 Jul 2013 10:28:52 -0500 >>> Subject: Re: [caret-users] F99 to MNI >>> Hi Pablo, >>> >>> Sorry -- this is the first I have heard of it. Pretty cool: >>> >>> http://www.bic.mni.mcgill.ca/ServicesAtlases/Macaque >>> >>> If someone has registered the F99 atlas to this one, I am unaware of it >>> (just as I was unaware of the MNI macaque atlas until you educated me). >>> >>> Donald McLaren registered his 112RM atlas to F99; that's here: >>> >>> MCLAREN_EtAl_2009 >>> http://sumsdb.wustl.edu/sums/directory.do?id=6716882 >>> >>> Donna >>> >>> >>> On Jul 8, 2013, at 9:01 AM, Pablo Barttfeld <[email protected]> >>> wrote: >>> >>> > Hi Donna, thanks for your response. >>> > Sorry I was not clear enough, I meant the macaque MNI space, not the >>> human MNI. >>> > thanks a lot >>> > Pablo >>> > >>> > >>> > 2013/7/8 Donna Dierker <[email protected]> >>> > I'm pretty sure you're the first person to ask that question. Or at >>> least the first I've heard it. >>> > >>> > Obviously the macaque and human brains have different scales, but it >>> might, in principle, be possible. Computing a volumetric transform from >>> the F99 individual monkey volume to either MNI305 or avg152T1 mean human >>> atlases doesn't seem likely to work well. >>> > >>> > But I think David registered the F99 surface to the same 73730 mesh as >>> the PALS human atlas. (He had a good reason for doing so.) If that is in >>> the Sept 2006 tutorial dataset, then you could load the F99 paint areas on >>> the PALS atlas and use Attributes: Paint to project them from surface-land >>> to volume-land, using the PALS flirt, SPM, or MRITOTAL surface as the >>> mapping substrate. >>> > >>> > Hopefully David will chime in if the F99-to-PALS correspondence makes >>> this a bad idea. >>> > >>> > (Let's face it: We must always approach cross-species registration >>> with a long list of caveats.) >>> > >>> > >>> > On Jul 8, 2013, at 4:37 AM, Pablo Barttfeld <[email protected]> >>> wrote: >>> > >>> > > Hi all, >>> > > I would like to map the regions in F99 into MNI space, is there a >>> function in Caret to do that? >>> > > Best >>> > > Pablo >>> > > >>> > > >>> > > _______________________________________________ >>> > > 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 >>> > >>> > _______________________________________________ >>> > 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 >>> >>> >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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