Re: [caret-users] FSL and Caret

2010-05-12 Thread Matt Glasser
Nonlinear registration certainly generates a resultant image that looks more like the template. In my opinion, it results in better alignment of structures and makes group analyses (e.g. fMRI, diffusion) more accurate, however this opinion is not universally shared (yet). High dimensional

Re: [caret-users] Similarity Index

2010-11-04 Thread Matt Glasser
What are you trying to show with this similarity index? Do you want a score saying how correlated two maps are, or something more? More details about what you are doing would help us to best answer your question. Peace, Matt. _ From: caret-users-boun...@brainvis.wustl.edu

Re: [caret-users] caret_command -volume-map-to-surface

2011-06-08 Thread Matt Glasser
It is possible to map 4D NIFTI files to a metric all at once, so you need not reference each frame individually. What scripting language is the below out of curiousity? Peace, Matt. _ From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu]

Re: [caret-users] Viewing time series data overlaid on surface

2011-08-09 Thread Matt Glasser
Splitting the volume is definitely not required though. Peace, Matt. -Original Message- From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Laumann, Timothy Sent: Tuesday, August 09, 2011 4:10 PM To: Caret, SureFit, and SuMS software

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

2011-12-16 Thread Matt Glasser
please contact her if you want to sign up. Best, Matt Glasser. Van Essen Lab. _ From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Colin Reveley Sent: Friday, December 16, 2011 12:51 PM To: caret-users@brainvis.wustl.edu

Re: [caret-users] FA-surefit

2012-01-10 Thread Matt Glasser
Hi Colin, I have used the mean of f (mean_f1samples + mean_f2samples + mean_f3samples) to make surfaces from diffusion data. I threshold the image and then do manual editing to clean it up. It is timeconsuming, but possible to get high quality surfaces from this. I would note that

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

2012-01-11 Thread Matt Glasser
it isn't in the uk actually. not that there is one. there isn't. -- Forwarded message -- From: Matt Glasser m...@ma-tea.com To: 'Caret, SureFit, and SuMS software users' caret-users@brainvis.wustl.edu Cc: Date: Tue, 10 Jan 2012 19:12:08 -0600 Subject: Re: [caret-users] FA

Re: [caret-users] segmenting with diffusion maps

2012-02-20 Thread Matt Glasser
I use the sum of f (i.e. sum 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 Reveley Sent: Sunday,

Re: [caret-users] segmenting with diffusion maps

2012-02-29 Thread Matt Glasser
: Contents of caret-users digest... Today's Topics: 1. Re: segmenting with diffusion maps (Matt Glasser) -- Forwarded message -- From: Matt Glasser m...@ma-tea.com To: 'Caret, SureFit, and SuMS software users' caret-users@brainvis.wustl.edu Cc: Date: Mon, 20 Feb 2012 09:15:03

Re: [caret-users] marmoset atlas

2012-03-16 Thread Matt Glasser
Unfortunately not. We'll have a chimpanzee atlas at some point in the future though. Peace, Matt. _ From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Colin Reveley Sent: Friday, March 16, 2012 7:40 AM To:

Re: [caret-users] myelin mapping

2012-04-22 Thread Matt Glasser
It would work to provide the image you want to use for the myelin map (i.e. the MTR) and then a volume of ones for the T2. Then format the ribbon volume like a FreeSurfer ribbon file (in terms of the numbers that correspond to particular labels). Peace, Matt. _ From:

Re: [caret-users] myelin mapping

2012-07-01 Thread Matt Glasser
lh.curv and rh.curv are made by mris_make_surfaces normally. You might as well use caret to remake the curvature files: caret_command -surface-curvature and then use mean curvature. You will want to make sure that the thickness matches your volumes, because it is used as a part of the

Re: [caret-users] myelin

2012-07-04 Thread Matt Glasser
The ribbon volume needs to have labels like the FreeSurfer ribbon volume (i.e. 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

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

2012-07-06 Thread Matt Glasser
Subject line so it is more specific than Re: Contents of caret-users digest... Today's Topics: 1. Re: myelin (Matt Glasser) -- Forwarded message -- From: Matt Glasser m...@ma-tea.com To: 'Caret, SureFit, and SuMS software users' caret-users@brainvis.wustl.edu Cc: Date: Wed, 4 Jul

Re: [caret-users] myelin, ribbon

2012-07-07 Thread Matt Glasser
The white matter is not needed. Peace, Matt. _ From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Colin Reveley Sent: Saturday, July 07, 2012 2:16 PM To: caret-users@brainvis.wustl.edu Subject: [caret-users] myelin, ribbon

Re: [caret-users] Myelin :(

2012-07-08 Thread Matt Glasser
I don't know. Perhaps you need to send me the data and commandline you are using for me to debug this. http://brainvis.wustl.edu/cgi-bin/upload_matt.glasser.cgi Peace, Matt. _ From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On

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

2012-08-28 Thread Matt Glasser
There is no tessellation algorithm in workbench, and it is unlikely there will one any time soon. 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

Re: [caret-users] caret-users Digest, Vol 108, Issue 1

2012-09-14 Thread Matt Glasser
Hi, Can you put an echo command around the command line that is failing? Thanks, Matt. From: Andrew Bock ab...@u.washington.edu Reply-To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Date: Friday, September 14, 2012 6:37 PM To: caret-users@brainvis.wustl.edu

Re: [caret-users] A precuneus cluster disappeared after surface projection

2012-09-17 Thread Matt Glasser
You would probably have the most success with a fully surface-based pipeline (i.e. project the minimally preprocessed time series on the individual subject's surfaces and analyze and average them there). This is something we are working on together with the FSL group to make available in the

Re: [caret-users] Question about MyelinMapping

2012-11-12 Thread Matt Glasser
I wonder if your sform has obliques in it. I agree that a screenshot would be helpful, together with verifying that the surfaces and T1w and T2w volumes are well aligned in some other screenshots. Peace, Matt. On 11/12/12 8:42 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Okay, if you're

Re: [caret-users] Question about MyelinMapping

2012-11-14 Thread Matt Glasser
: mydata_originalT1w) T2w FSLview / our data (file name: mydata_T2w) I wonder if the phase/frequency encoding caused the difference. Is there any other point I have to check or change? Sincerely. Yuichiro Shimizu 2012/11/13 Matt Glasser m...@ma-tea.com I wonder if your sform has obliques in it. I agree

Re: [caret-users] Question about MyelinMapping

2012-11-15 Thread Matt Glasser
Shimizu 2012/11/13 Matt Glasser m...@ma-tea.com I wonder if your sform has obliques in it. I agree that a screenshot would be helpful, together with verifying that the surfaces and T1w and T2w volumes are well aligned in some other screenshots. Peace, Matt. On 11/12/12 8:42 AM, Donna

Re: [caret-users] Quetion about data acquisition

2012-11-29 Thread Matt Glasser
You'd have to ask the NAMIC people about the bandwidth for their scans. I provided all the information I could find on that data. I'm not sure what scans you are varying the parameters of there. Did you use percentile scaling? The bias fields are not really dependent on most parameters. The

Re: [caret-users] Mapping Microscopic, Neuroanatomic Data onto Caret

2012-12-14 Thread Matt Glasser
There is a Brodmann map. You can make surface maps in which you set all the vertices of a given parcellation to have some quantitative value. If you have a spreadsheet of Brodmann areas by measure this can be done. When I did this for some other study, I did it all in matlab and just saved out

Re: [caret-users] Sequences for myelin mapping

2013-05-08 Thread Matt Glasser
I don't think we have figured out how to make FreeSurfer data run with oblique sforms line up with volume data in Caret. I have avoided this issue by always removing the oblique sforms before running FreeSurfer. In theory, it must be possible to fix, however the different software handle the

Re: [caret-users] painting

2013-05-26 Thread Matt Glasser
Connectome Workbench can write a label table into a NIFTI volume via a header extension: wb_command -volume-label-import Peace, Matt. On 5/25/13 4:38 PM, do...@brainvis.wustl.edu do...@brainvis.wustl.edu wrote: This is trickier, because there is no standard file format that specifies label

Re: [caret-users] wb FSL fibre volume display

2013-06-14 Thread Matt Glasser
That is right this is all unsupported. The main reason is that we are going to be making changes to the file formats and don't really want the temp formats propagating themselves too widely. We do hope for the next workbench release (after the one happening imminently) have all this sorted out

Re: [caret-users] wb FSL fibre volume display

2013-06-14 Thread Matt Glasser
Hi Tim, I think workbench and Caret have the same limitations for the particular issue he is having (namely that the fibres ARE free from voxel centers). Its possible I misunderstood him though. Matt. From: Timothy Coalson tsc...@mst.edu Reply-To: Caret, SureFit, and SuMS software users

Re: [caret-users] F99 to MNI

2013-07-08 Thread Matt Glasser
I cannot imagine being able to do this well with volumetric registration. Matt. On 7/8/13 8:54 AM, Donna Dierker do...@brainvis.wustl.edu 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

Re: [caret-users] wb functionality

2013-07-14 Thread Matt Glasser
a) Flat maps display fine in Connectome Workbench, though we don't really use them much. We have been bringing standard ones onto the relevant FS_LR meshes. b) Tim will reply in detail to this question. c) This diffusion stuff is still unsupported, but we hope to get it finalized this summer.

Re: [caret-users] transforming surf.gii

2013-08-22 Thread Matt Glasser
Try updating to the latest matlab GIFTI reader and see if that helps. Peace, Matt. From: Colin Reveley cm...@sussex.ac.uk Reply-To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Date: Thursday, August 22, 2013 4:33 PM To: caret-users@brainvis.wustl.edu

Re: [caret-users] mapping fMRI maps generated in freesurfer on

2013-11-07 Thread Matt Glasser
You need to save the file as a GIFTI .func.gii file. Then you can use the fsaverage to FS_LR and FS_LR to PALS deformation maps to resample the data onto the PALS mesh. Peace, Matt. From: SHAHIN NASR sha...@nmr.mgh.harvard.edu Reply-To: Caret, SureFit, and SuMS software users

Re: [caret-users] display myelin mapping results

2014-02-05 Thread Matt Glasser
There is probably some issue with the headers on these data. You could try running fslreorient2std before running this pipeline (including FreeSurfer). Peace, Matt. On 2/5/14 8:52 AM, Cheng, Hu huch...@indiana.edu wrote: Thanks Donna. Yes, I did use overlay, I was able to see the

Re: [caret-users] display myelin mapping results

2014-02-07 Thread Matt Glasser
] On Behalf Of Matt Glasser Sent: Wednesday, February 05, 2014 10:24 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] display myelin mapping results There is probably some issue with the headers on these data. You could try running fslreorient2std before running this pipeline

Re: [caret-users] Myelin mapping

2014-03-09 Thread Matt Glasser
It's possible it is trying to write something to the current directory and you don't have permission to write there. Peace, Matt. On 3/9/14 2:02 PM, Righart, Ruthger righ...@lrz.tu-muenchen.de wrote: Dear Caret experts, I would like to perform myelin mapping following the descriptions on the

Re: [caret-users] question about myelin mapping

2014-03-14 Thread Matt Glasser
Do the volumes align with the surfaces? Did you remove any oblique sforms? Peace, Matt. On 3/14/14 8:01 AM, Righart, Ruthger righ...@lrz.tu-muenchen.de wrote: Dear Caret experts, I am using Caret for myelin mapping and I got first results for 4 subjects. After loading MyelinMapping.metric in

Re: [caret-users] caret-users Digest, Vol 124, Issue 6

2014-03-19 Thread Matt Glasser
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. Re: question about myelin mapping (Matt Glasser

Re: [caret-users] Surface-Volume registration

2014-03-28 Thread Matt Glasser
Did you remove the sform and qform at the beginning of the process (i.e. before FreeSurfer)? Peace, Matt. On 3/28/14, 9:04 AM, Righart, Ruthger righ...@lrz.tu-muenchen.de wrote: Dear Caret experts, I am working on myelin mapping but encounter errors in surface-volume registration, as

Re: [caret-users] caret-users Digest, Vol 124, Issue 15

2014-03-28 Thread Matt Glasser
: 1. Re: Surface-Volume registration (Matt Glasser) -- Message: 1 Date: Fri, 28 Mar 2014 09:58:32 -0500 From: Matt Glasser m...@ma-tea.com To: Caret, SureFit, and SuMS software users caret-users

Re: [caret-users] caret-users Digest, Vol 124, Issue 15

2014-03-28 Thread Matt Glasser
0.00 0.00 1.00 ... and the same exact values for the sform matrix I don't think the exact values of the last column matter much at this point, since I don't think you've done volume registration yet. Tim On Fri, Mar 28, 2014 at 3:09 PM, Matt Glasser m...@ma-tea.com wrote: All

Re: [caret-users] Myelin Mapping

2014-07-31 Thread Matt Glasser
Please paste the output of fslhd on both files. Peace, Matt. From: SHAHIN NASR sha...@nmr.mgh.harvard.edu Reply-To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Date: Thursday, July 31, 2014 at 11:18 AM To: Caret, SureFit, and SuMS software users

Re: [caret-users] Myelin Mapping

2014-07-31 Thread Matt Glasser
It may not be capable of working with images that are not LPI or RPI. I¹d also note that hopefully within the next week or two the HCP pipelines will be released and this code will become unsupported (since the HCP pipelines make myelin maps much better). Peace, Matt. On 7/31/14, 1:31 PM,

Re: [caret-users] Myelin Mapping: different number of nodes

2014-12-18 Thread Matt Glasser
Hi Eileen, This version of myelin mapping is no longer supported. Please use the HCP Structural Pipelines to create your myelin maps: https://github.com/Washington-University/Pipelines Thanks, Matt. From: Eileen Moore eimo...@mail.sdsu.edu Reply-To: Caret, SureFit, and SuMS software users

Re: [caret-users] Missing parts in MyelinMap+Different number of nodes!

2015-06-20 Thread Matt Glasser
, rather than this (older generation) caret-based myelin mapping script: http://www.humanconnectome.org/documentation/HCP-pipelines/ This also has the advantage of writing output files in workbench formats, rather than older caret formats. I have a hunch that Matt Glasser will point you

Re: [caret-users] Sucessor to caret

2016-01-19 Thread Matt Glasser
Though not all yet available publicly, I think the software that is succeeding caret will work for the vast majority of users, even those doing non-human primate work. Peace, Matt. From: on behalf of Kevin Aquino Reply-To:

Re: [caret-users] info in the deformation maps

2017-10-20 Thread Matt Glasser
Also Connectome Workbench has some more advanced methods of quantifying isotropic and anisotropic registration induced distortion. Peace, Matt. From: on behalf of Timothy Coalson Reply-To: "Caret, SureFit, and SuMS software users"

Re: [caret-users] info in the deformation maps

2017-10-20 Thread Matt Glasser
It¹s also worth noting that in Connectome Workbench we moved away from the deformation map file as it enforces a particular resampling of the data as well (not just a data transformation). Instead we use the deformed and target spheres to store the registration and this allows for choice in