[caret-users] re hi res recon

Hi - in order to work with hi res monkey data (250um) I manually removed the cerebellum and hindbrain. there was no skull etc. similarly for freesurfer. surefit might take some time. It did work with manual removal and a lot of time manually editing voxels. downsampling to 1mm and running

Re: [caret-users] cocomac

On 8 March 2014 21:47, Colin Reveley cm...@sussex.ac.uk wrote: Thanks matt I was unaware of that thing in matlab by Gleb. There is also scalablebrainatlas and cocomac2 which is all great. staying within caret as the software substrate, and although it's not linked to cocomac (yet), Markov et

Re: [caret-users] cocomac

Thanks matt I was unaware of that thing in matlab by Gleb. There is also scalablebrainatlas and cocomac2 which is all great. staying within caret as the software substrate, and although it's not linked to cocomac (yet), Markov et al's recent stuff is on F99. their site is corenets. It may be of

Re: [caret-users] libstdc++ version and caret5 (Timothy Coalson)

That's very helpful Tim/John thanks. Can I confirm it should (at least probably) run on RHEL6 and clones (CENTOS) too? I can't test it it's for downstream colleagues. For delivering a product using caret5 (and workbench). that's very handy the RHEL5 compilation. thanks. We had the same issue a

Re: [caret-users] F99 paxinos paint vol

In addition, depending on your needs you may find some of the services at scalablebrainatlas.incf.org to be useful there are volume projections of paxinos and others from caret onto F99 but with a subtler representation of the cortical thickness than caret's mapping permits. you can download the

Re: [caret-users] ribbon generation

Subject: Re: [caret-users] ribbon generation I think we may have intended workbench-related things to go on hcp-users, but I'm not sure. I know, but this is actually more caret related. caret is the software I'll use for the myelin mapping. workbench might play an ancillary role but doesn't

[caret-users] ribbon generation

an accurate ribbon. I can get one, but I can't figure out how to size and align it when I can't use mris_fill -c best, Colin Reveley ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users

[caret-users] cifti math mem

Hi - I'm wondering (before I try and damage remote equipment) when running wb_command -cifti-math is it necessary that the cifti(s) fit into RAM memory? what I want to do is take a very large dconn.nii file, and binarize it such that all non-zero entries are 1 and all 0 entries stay 0. this

Re: [caret-users] transforming surf.gii

!! best, Colin On 22 August 2013 22:33, Colin Reveley cm...@sussex.ac.uk wrote: I should say: it loads in workbench. it just doest work. images (gifti in matlab, same in workbench) attached. also the header I'm trying to load. You'll see the header has quite a lot of detritus. best Colin

Re: [caret-users] transforming surf.gii

. It does look like endianness to the eye. Since surf2surf 5.04 resolves it I'll look at what changed. thanks again Colin On 23 August 2013 16:23, Colin Reveley cm...@sussex.ac.uk wrote: actually it seems as simple as surf2surf -i problem.surf.gii -o fixed.surf.gii appears to fix it up so

[caret-users] transforming surf.gii

hi. we have a system (a bespoke system) for non-linear registration of volumes. we wondered if we could take the output transform and use that data to shift the vertices of a surf.gii so that it's transformed. much like wb_command and fnirt. we tried it. in matlab (using gifti lib) it works.

[caret-users] paint vols and afni

When one saves a paint volume in caret as a nifti, there are two header extensions that reflect the value-name mapping. One of these is an afni header extension. It is marked as deprecated. But is it something one could actually load in afni itself (obviously the data can be loaded, but can it

Re: [caret-users] caret command not found

first: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/installation/caret5_installation.html if you installed caret using a package manager, first check in your package manager that caret_command is installed. It might be a separate package to caret. Also make sure it's version 5.64 or

Re: [caret-users] caret-users Digest, Vol 115, Issue 7

, Issue 6 (Colin Reveley) -- Forwarded message -- From: Matt Glasser m...@ma-tea.com To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Cc: Date: Fri, 14 Jun 2013 14:56:32 -0500 Subject: Re: [caret-users] wb FSL fibre volume display Hi Tim, I think

Re: [caret-users] caret-users Digest, Vol 115, Issue 2

given that fslview 4 (AFAIK) is not on mac yet, this would appear germane to the world at large. but a bit cryptic. what does this have to do with vertices? what, rather more explicitly, is the gist you speak of? a bug? in what software? what conditions? fslview 3 looks like it might be

Re: [caret-users] label volume mapping

May 2013 02:52, Colin Reveley cm...@sussex.ac.uk wrote: Hi - re: wb_command -volume-label-import what it appears to do is just vaporize the header. However, much could have gone wrong. The input volume is wholly constructed in software (mainly imageJ and inhouse C) and is probably weird

Re: [caret-users] label volume mapping

/plugins/mwiki/index.php/cifti:ConnectivityMatrixFileFormats While I still tend to be very caret5-centric, because I'm wrapping up a multi-year project started in caret5, I know I need to start understanding this stuff. On May 29, 2013, at 10:40 PM, Colin Reveley cm...@sussex.ac.uk wrote

Re: [caret-users] label volume mapping

Hi - re: wb_command -volume-label-import what it appears to do is just vaporize the header. However, much could have gone wrong. The input volume is wholly constructed in software (mainly imageJ and inhouse C) and is probably weird (although it's been saved in CARET before trying to run this.

Re: [caret-users] label volume mapping

, controlled (by us) distributable method of doing this in software that we can be confident of distributing to users in a way that is automated. Good Software Engineering Practice. Or something. best, Colin On 30 May 2013 02:52, Colin Reveley cm...@sussex.ac.uk wrote: Hi - re: wb_command

Re: [caret-users] labels

Well that certainly is enormously helpful, thanks Matt. There's certainly lots of interesting looking commands in wb now. That bingham estimation thing is especially intriguing. On a separate note: I've got a huge label.gii file. It's from a caret surface registration. I want to extract just

[caret-users] contours

a) Is it possible to make a surface from saggital or horizontal sections, rather than coronal sections? b) when drawing contours to make a surface, is it required that the contours be midthickness, or can one trace a white matter boundary? Needless to say, I have a reason (or imagine I do) task

Re: [caret-users] contours

thanks re: saggital and horizontal: forget that then. so the question returns to: can I use contours as a mechanism to correct artifact in the mri and make a wm segmentation that is helpful? I RTFM (the caret tutorial dated about 2008) on contours and while the examples are midthickness it

[caret-users] openGL

Hi, Typically, at an utterly curicial juncture my macbook pro has blown it's GPU. The computer just gets too heavily used. Anyway, it has two: an on-board intel and the ATI on the pcibus (I never liked ATI. I paid $3000 for this machine less than a year ago.) they are obliged to fix it. but

Re: [caret-users] transforms

managing the list at caret-users-ow...@brainvis.wustl.edu When replying, please edit your Subject line so it is more specific than Re: Contents of caret-users digest... Today's Topics: 1. Re: transforms (Colin Reveley) 2. Re: transforms (Timothy Coalson) 3. Re: transforms (Donna

Re: [caret-users] flipping

Jet lagged though i am it is clear that any image is trivially flippable. so that's solved short term, sorry. in the long term, it is definitely best to change all my caret data to the correct hemispheric designation and orientation. but I think it's not hard: flip surfaces in y with a

Re: [caret-users] orientation

thanks Rouhollah but those don't quite cover it. and anyway, I'd prefer to keep freesurfer out of it. I think restricting to metric etc and generally the strategy I outlined in my follow up is probably decent. a simple approach that captures most stuff in a simple way, and just ignores scenes,

Re: [caret-users] metric scaling

Cc: Date: Wed, 7 Nov 2012 09:30:35 -0600 Subject: Re: [caret-users] metric scaling I don't know of an easier way. Knowing me, I'd do: caret_command -metric-information my.metric | grep my column name # hack with cut to get just the sample deviation caret_command -file-convert

Re: [caret-users] spec print issue

with the right names are there. there's no file missing error. but I find it confusing that it always creates a new areacolor file when I start caret, rather than use the one I put in the spec. thanks.. Colin On 2 November 2012 18:52, Colin Reveley cm...@sussex.ac.uk wrote: does anyone know

Re: [caret-users] spec print issue

with areacolor files? I make sure files with the right names are there. there's no file missing error. but I find it confusing that it always creates a new areacolor file when I start caret, rather than use the one I put in the spec. thanks.. Colin On 2 November 2012 18:52, Colin Reveley

Re: [caret-users] caret-users Digest, Vol 107, Issue 8

it is more specific than Re: Contents of caret-users digest... Today's Topics: 1. Re: inner white matter (Donna Dierker) 2. Re: caret-users Digest, Vol 107, Issue 7 (Colin Reveley) 3. Re: inner white matter (Timothy Coalson) -- Forwarded message -- From: Donna Dierker do

Re: [caret-users] caret-users Digest, Vol 107, Issue 10

. This is because we are using FreeSurfer to generate surfaces now and focusing our development on new things related to brain connectivity. If you sent me one of your images I could see if I can think of any way to make it more palatable for FreeSurfer... Peace, Matt. From: Colin Reveley cm

Re: [caret-users] caret-users Digest, Vol 107, Issue 7

So to be just totally clear: what I actually want is this: If you look at the figures I attached you'll see two main components: the gm and wm, characterised by signal intensity. We can use that to make a line at the wm/gm and another at pial and we obtain two surfaces enclosing the gm. But in

[caret-users] Inner white matter

Would it be possible to shrink a surface with a scaling matrix, and then define the mesh as being in the same space as the original. E.g a mesh at 1mm scaled down to eg 0.25mm and then redefined as a 1mm surface? The notion here is to generate an outer and inner pair of white matter surfaces. Of

Re: [caret-users] caret-users Digest, Vol 106, Issue 21

. I'm not certain that this will work, but I suspect that it (or some variation therof) will finally get the job done for you. David On Jul 21, 2012, at 3:18 PM, Colin Reveley wrote: the only thing that works without making a new surface is smoothing operations on parts of the ROI

Re: [caret-users] medial wall issue

, please edit your Subject line so it is more specific than Re: Contents of caret-users digest... Today's Topics: 1. Re: caret-users Digest, Vol 106, Issue 18 (Colin Reveley) -- Forwarded message -- From: Colin Reveley cm...@sussex.ac.uk To: caret-users

Re: [caret-users] caret-users Digest, Vol 106, Issue 18

to surfaces made in caret with surefit as well as FS stuff, although less so. On 21 July 2012 21:09, Colin Reveley cm...@sussex.ac.uk wrote: in may cases it is very, VERY hard to paint the apropriate subset of nodes, if the geometry is truly complex. one must use many little borders instead

Re: [caret-users] caret-users Digest, Vol 106, Issue 11

@brainvis.wustl.edu Cc: Date: Mon, 16 Jul 2012 09:18:37 -0500 Subject: Re: [caret-users] linear surface transforms The honest answer to most of these questions is I don't know; however, see inline comments below for any hints I think are worth sharing. On Jul 15, 2012, at 7:56 AM, Colin Reveley

[caret-users] linear surface transforms

Before I begin something that's going to be tough, may I just confirm: I've got a structural and other (diffusion related) volumes, all in register, at 250um. I need to make wm and pial surfaces in freesurfer, average them, and then map the structural (myelin) and diffusion stuff using matt's

[caret-users] Myelin :(

I'm really, really sorry I can't figure this out. I made a ribbon as close to berts as I could using mri_ribbon to get the estimate of the gm on each side, and then manual manipulation to add them as one volume with the region inside coloured as berts wm. some bits between gyro that should be o

Re: [caret-users] Myelin :(

, Colin Reveley wrote: I'm really, really sorry I can't figure this out. I made a ribbon as close to berts as I could using mri_ribbon to get the estimate of the gm on each side, and then manual manipulation to add them as one volume with the region inside coloured as berts wm. some bits between

Re: [caret-users] caret-users Digest, Vol 106, Issue 4

. the specific numbers for grey matter). Also, what is your commandline? ** ** Peace, Matt. ** ** -- *From:* **caret-users-boun...@brainvis.wustl.edu** [mailto:** caret-users-boun...@brainvis.wustl.edu**] *On Behalf Of *Colin Reveley *Sent:* Wednesday

Re: [caret-users] myelin

forgot 4th july... tried a few more things: make all vols -++ (FSL style) put MTR into intensity range of t1/t2 as described in matt's paper (no dice). then, add one to that mtr and use a vol of all ones as t2 so divide by zero is impossible, ever. (no dice) take that mtr from previous step,

[caret-users] more marmoset

I agree that a WM and PIAL from freesurfer is the way to go with marmoset. For what it's worth, if you calls it a galago (in caret) and uses a 300um MTR you can get a halfway decent surface (not really that good, but it works). at 300um caret successfully get's rid of the hindbrain. If I could

[caret-users] myelin mapping

Hi - I had a data accident a while ago. I lost a freesurfer dir. But, since I was importing to caret I have lh and rh white and pial from freesurfer, and I have the thickness files for each. And I have the appropriate MRIs. These files took a LONG time to get right, and then it took quite a

Re: [caret-users] border update

caret 5.65 won't even run on rhel 5.7 unless you mess with glibc. I installed an older version for colleague. graphics driver or not, rhel4 may be a bit ill advised at this point. and drawing borders is counterintuitive and hard and slow before you get familiar. and it might have the odd bug, I

[caret-users] metric sum

Hello. If I have a surface with some paints on it and a metric on it, then I can select the nodes where the paint is P and within P the metric is non-zero. and I can do all kinds of stuff subsequently with this subset of nodes (metric present in region). I can find the mean, std, etc. I can

[caret-users] summing

sorry - I'm very tired here and not at all able to think at all. zombie. presumably if I know how many nodes there are, and I know the mean value then the sum is the mean times the number of nodes, since the mean is the sum divided by the number. ___

[caret-users] paxinos reg

Hello - in the caret demo and elsewhere there's a surface, topologically correct on 73730 that was made from sections of the paxinos atlas. So, It's an odd looking hemisphere, but it has the virtue of reflecting the text. there's also another somehere I think I recall that's not topologically ok

[caret-users] segmentation

Hi - I know there is a new version of caret in the works, and I know that it is part of the connectome project, and therefore will likely have more features related to tractography. I'm looking forward to that hugely. I was wondering what features it might have regarding segmentation. Caret is

Re: [caret-users] caret-users Digest, Vol 102, Issue 11

wall in the GUI (border, paint, roi ooeration, select nodes by paint, smooth nodes) trying to make it as similar to F99 as possible before I register. this issue doesn't seem to trouble others as much as me. hope helps On 20 March 2012 18:06, Colin Reveley cm...@sussex.ac.uk wrote: Tristan

Re: [caret-users] caret-users Digest, Vol 102, Issue 11

And sorry - it's just occurred from Tristan's description: you are not registering anatomy exactly. you are registering topological features. The surface represents a brain sure enough, but the registration algorithm registers gross anatomy/topology. It could be some other manifold. and that

[caret-users] marmoset atlas

I wonder, is there a caret atlas for any marmoset anatomy? There was a discussion a little while back regarding the construction of an atlas for a new species. Is that in fact common marmoset? will it be publicly available if so? I am presenting my own work to a lab in late june. the lab is

Re: [caret-users] marmoset

at caret-users-ow...@brainvis.wustl.edu When replying, please edit your Subject line so it is more specific than Re: Contents of caret-users digest... Today's Topics: 1. .annot or .label conversion to caret (Sam Carpenter) 2. marmoset atlas (Colin Reveley) 3. Re: .annot or .label

Re: [caret-users] ima

all those programs are nice (there's also miconv which you can get from the ubuntu or debian or neurodebian package manager, or by compiling odin which is some sort of thing. not sure what, but it comes with miconv. miconv is really good for DICOMM and other low level stuff, and understands

Re: [caret-users] ima

this will work for your issue very quickly. On 13 March 2012 08:14, Colin Reveley cm...@sussex.ac.uk wrote: all those programs are nice (there's also miconv which you can get from the ubuntu or debian or neurodebian package manager, or by compiling odin which is some sort of thing. not sure

Re: [caret-users] caret-users Digest, Vol 101, Issue 16

On Fri, Feb 17, 2012 at 11:02 AM, Colin Reveley cm...@sussex.ac.uk wrote: Tim - what you say is interesting. I have actually wondered about node spacing in fiducial surfaces registered to F99 via macaque.sphere6. It's not always 100% super straight forward to register (without lots

Re: [caret-users] caret-users Digest, Vol 101, Issue 13

of mean_f#samples) from bedpostx. It will still require a fair amount of manual intervention. ** ** Peace, Matt. ** ** -- *From:* **caret-users-boun...@brainvis.wustl.edu** [mailto:** caret-users-boun...@brainvis.wustl.edu**] *On Behalf Of *Colin

Re: [caret-users] Interspecies comparisons - creating a new atlas for a different primate species

the menu driven landmark pinned reg. Other than fiducials (WM,GM, mean) the topos and other surfaces are made with caret operations. I'm guessing if I repeat those operations with caret5.65, it will follow the new scheme of things in terms of how node spacing is decided? Colin Reveley, sussex. On 17

Re: [caret-users] caret-users Digest, Vol 101, Issue 2

One would expect the caret GUI to become unresponsive, and also expect the process to be listed as not responding in the task manager even if things were going well. but it crashes. might I suggest the neurodebian virtual machine? there is a 32bit windows version. Loads of great stuff on there

Re: [caret-users] caret-users Digest, Vol 100, Issue 7

we are working on together with Oxford. ** ** Peace, ** ** Matt. ** ** -- *From:* **caret-users-boun...@brainvis.wustl.edu** [mailto:** caret-users-boun...@brainvis.wustl.edu**] *On Behalf Of *Colin Reveley *Sent:* Tuesday, January 10

[caret-users] FA-surefit

Before I hit my head against it pointlessly, but because there could be value in it, how much luck am I likely to have have in making a surface from a fractional asisotropy volume, or similar (something non-tensor that's a bit more complicated but still FA like to the eye, or else eg mean

[caret-users] painting the entire GM thickness accurately from surface data

Hi - (happy new year) Caret has a nice feature that lets you drop paints from a surface into a volume. but one thing is that all it really allows is for one to specifiy a distance above and below the suface. So, it does not allow one to fill the gray matter of a volume with paint accurately.

[caret-users] DWI, trackvvis, metric autoload

Hi - Caret has a feature metric auto load intended for tractography data. Essentially, for each voxel in a volume there's an associated metric. When you click a surface node, the metric for the node associated with that voxel is loaded. That suits me well, and works well for probabilistic

Re: [caret-users] DWI, trackvvis, metric autoload

and targets for more serious analysis of the DWI data, which you then express as a metric. On 16 December 2011 18:36, Colin Reveley cm...@sussex.ac.uk wrote: Hi - Caret has a feature metric auto load intended for tractography data. Essentially, for each voxel in a volume there's an associated metric

[caret-users] hi res macaque

Hello. I have macaque data that is 0.25mm. I like that. I can do things with it that are more than cosmetic. The data was taken with a fancy brukker, and the contrast is very good from the sequence used. so good I wonder if it's a problem (it's a FLASH_MTR - it does correlate to T1 really

Re: [caret-users] caret-users Digest, Vol 94, Issue 10

: [caret-users] caret-users digest, surface tip mmissing On 07/23/2011 01:31 PM, Colin Reveley wrote: strictly, no tissue is missing - it's just compacted, and the remaiing tip is angled down. so one strategy would be: just forget it. you've seen the surface I've made in prior mails

Re: [caret-users] caret-users Digest, Vol 94, Issue 4

...@brainvis.wustl.edu You can reach the person managing the list at caret-users-ow...@brainvis.wustl.edu When replying, please edit your Subject line so it is more specific than Re: Contents of caret-users digest... Today's Topics: 1. segmentation for surf morphometry issue (Colin Reveley

[caret-users] QT issue + tracer metric to regional area

Two questions, if you'd be kind enough: 1) GUI issue I've been using Caret for a while now. There is one niggle. I'm using ubuntu 10.04 64 bit. As you mentioned, the older version of caret that ships with this linux distribution has a couple of problems rendering files, and crashes sometimes.