Re: [caret-users] SumsDB website can't be reached

2016-06-28 Thread Donna Dierker
It sure would be nice if sumsdb were working right now, but it's not, and I have no quick-fix for getting it to work (though we are discussing ideas). Meanwhile, I'd like to narrow down which F99 individual to F99 registration dataset you were looking for. If you segmented your monkey's brain

Re: [caret-users] SumsDB website can't be reached

2016-06-27 Thread Donna Dierker
Hi Ting-Yu, Hopefully, someone will be able to provide the reference and a link to the dataset for registering individual monkeys to the F99 atlas. If not, I'll dig around tomorrow and try to find it. But I did want to let you know we are aware of the problem with sumsdb. Others have

Re: [caret-users] (no subject)

2016-03-24 Thread Donna Dierker
Hi Pavel, Caret cannot segment newborn cortex, but it can flatten hemispheres segmented using other software (e.g., LIGASE - http://brainvis.wustl.edu/LIGASE). I thought Fischl et al. were in the process of adding infant segmentation to Freesurfer. Don't know where that stands, but well worth

Re: [caret-users] Macaque Paxinos borders on flat map

2016-02-19 Thread Donna Dierker
Hi Julia, No one has answered your question yet, because it doesn't have a simple answer. It depends on what you are trying to do, and it might make more sense to work in workbench, rather caret, depending on what you are doing. If you have a label.gii, for example, you can view that in

Re: [caret-users] Sucessor to caret

2016-01-19 Thread Donna Dierker
Hi Dr. Aquino, No, Connectome Workbench does not offer features like segmentation or registration (though it does have wb_command features for resampling and related functions, e.g., -surface-project-unproject). Our lab typically uses software derived elsewhere for segmentation (e.g.,

Re: [caret-users] Generating cortical hull surface

2016-01-14 Thread Donna Dierker
> try to see what else may work for my sheep brains. > > Thanks again for all the help. > > Cheers, > Rosita > > On Tue, Jan 12, 2016 at 3:41 AM, Donna Dierker <do...@brainvis.wustl.edu> > wrote: > Hi Rosita, > > None of the parameters in these commands ma

Re: [caret-users] Generating cortical hull surface

2016-01-11 Thread Donna Dierker
minal so I use caret > > command executor. So, I wrote the name of the used command and their > > inputs > > as well as the complete command. > > > > Thanks again! > > > > Cheers, > > Rosita > > > > > > On Wed, Jan 6, 2016

Re: [caret-users] Generating cortical hull surface

2016-01-05 Thread Donna Dierker
the volume (output_volume.nii file created using SURFACE TO SEGMENTATION > VOLUME), it includes just few voxels in a raw. > > Any help would be greatly appreciated. > > Thanks, > Rosita > > > On Thu, Sep 3, 2015 at 12:36 PM, Donna Dierker <donna.dier...@sbcglobal.net

Re: [caret-users] LEFT HEM in FS-to-F99 Tutorial

2015-12-23 Thread Donna Dierker
Hi Julia, I confess I don't know these scripts inside and out, but this image is enlightening: http://brainvis.wustl.edu/pipermail/caret-users/attachments/20151222/180ba486/attachment-0001.png It looks like there is a hole in the surface at the occipital pole -- almost like perhaps Caret cut

Re: [caret-users] medial wall override via caret_command

2015-08-20 Thread Donna Dierker
!!! Daniel On 8/19/15, 6:38 PM, caret-users-boun...@brainvis.wustl.edu on behalf of Donna Dierker caret-users-boun...@brainvis.wustl.edu on behalf of do...@brainvis.wustl.edu wrote: Could you elaborate on how you are using caret_command? The Enable Medial Wall Override affects display

Re: [caret-users] doubt regarding fiducial mapping

2015-08-19 Thread Donna Dierker
you're shifting the volume or surface, and I always get confused about it. Usually I try it one way; look at the result like the capture below; and if it looks worse, I try it the other way. ;-) One of the ways usually does the trick. Donna On Aug 12, 2015, at 9:14 AM, Donna Dierker do

Re: [caret-users] doubt regarding fiducial mapping

2015-08-11 Thread Donna Dierker
What software was used to reconstruct the surface? With freesurfer, there is an offset between the orig.mgz and the surface. And depending on many factors, you might have to flip/rotate the surface to be in the same orientation as the volume (or bring the volume to the surface). See this

Re: [caret-users] doubt regarding fiducial mapping

2015-08-10 Thread Donna Dierker
This almost always is because the functional volume is not stereotactically registered to the anatomical volume used to generate the fiducial surface. Is this an atlas surface (e.g., one of the PALS mean midthickness surfaces), or is it an individual's surface reconstruction? If atlas, this

Re: [caret-users] statistical report on areal enlargement

2015-06-29 Thread Donna Dierker
Hi Leonardo, It is possible that one more skilled than I could get Statistical Paint Report to do what you want with less trouble. But for me, scripting it via the command line would be more straightforward. Have a look at two scripts here:

Re: [caret-users] Flattened Brain visulazation

2015-06-26 Thread Donna Dierker
Hi Adnan, I have run into those kinds of errors, and it can be very puzzling/frustrating. A couple of common triggers: * If you have a non-english character set installed on your computer/login, then this can sometimes cause read/write issues. Removing the non-english character set sometimes

[caret-users] New Paid Fellowships at the Mozilla Science Lab

2015-06-24 Thread Donna Dierker
From: Bill Mills b...@mozillafoundation.org Date: Tuesday, June 23, 2015 at 4:17 PM To: Software Carpentry Discussion disc...@lists.software-carpentry.org Subject: [Discuss] New Paid Fellowships at the Mozilla Science Lab Hi folks, We're very excited to announce that applications are

Re: [caret-users] negative values displayed positive

2015-06-22 Thread Donna Dierker
PM, Frédéric Roux f.r...@bcbl.eu wrote: Hi Dona, thanks for getting back on this. I am using NIFTI, so nothing rare from that side. Just uploaded the file via the link you sent me. Thanks for looking into this. -- FR - Original Message - From: Donna Dierker do

Re: [caret-users] negative values displayed positive

2015-06-21 Thread Donna Dierker
: Saturday, June 20, 2015 11:37:53 PM Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of nodes! Yes please use the HCP pipelines for myelin mapping. Peace, Matt. On 6/19/15, 4:17 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Xara, Because you

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

2015-06-19 Thread Donna Dierker
Hi Xara, Because you are in the enviable position of having high res T1 AND T2, you may be able to use the Human Connectome Project pipelines on your data, rather than this (older generation) caret-based myelin mapping script: http://www.humanconnectome.org/documentation/HCP-pipelines/ This

Re: [caret-users] Colours and scaling

2015-06-11 Thread Donna Dierker
Hi Pavel, Map your volume as a Paint ROI volume, rather than as a metric. Then use Attributes: Area Color to assign colors. Save not only the resulting paint file, but also the area color file. The paint file has the index to name mapping, while the area color maps name to color. If you're

Re: [caret-users] labelling of exported paint volumes

2015-05-22 Thread Donna Dierker
Hi Leonardo, Given the nature of the data you are mapping, I would expect fragmentation. This thread might help: http://brainvis.wustl.edu/pipermail/caret-users/2014-August/006199.html Hcp-users might yield more feedback on other strategies for accomplishing your goals. Cheers, Donna On

Re: [caret-users] change color metric overlap

2015-02-06 Thread Donna Dierker
Using either Surface: Region of interest or caret_command (-surface-region-of-interest-selection and -paint-assign-to-nodes), you can threshold your metrics at some value and assign a paint/llabel/ROI to them. Your paint name might be visual or auditory, but it gets mapped to an integer when

Re: [caret-users] problem with mapping volume to surface

2015-01-29 Thread Donna Dierker
First, make sure the computer you're using doesn't have a non-English character set installed, because that often interferes with the Qt file I/O. Second, make sure the spec file you're selecting has write permission. If necessary, copy it to a different filename and make sure it is writeable.

Re: [caret-users] Problemout of memory, please help me, thank you !

2015-01-12 Thread Donna Dierker
Scroll down to the Windows XP section: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/installation/caret5_installation.html But that out of memory error still makes me wonder about the character set. Unless you have a user/pc that has only an english character set that you could try

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2015-01-08 Thread Donna Dierker
it in Matlab with gifti.m (from the GIFTI toolbox). I then have all 19 columns at once! Now you have to ponder which are useful to you. Kind regards, Rikkert P.S. I noticed that in the Paxinos atlas, V5 is merged with the medial wall. On Thu, Jan 8, 2015 at 3:51 PM, Donna Dierker do

Re: [caret-users] metric user scale with fixed step size

2014-12-11 Thread Donna Dierker
You have six bins, like below, but compressed to 0:1? Hmmm. Scratching my head on that one. On Dec 11, 2014, at 9:30 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi Donna, I followed your advice and compressed the scale into 0:1. One more question: While the colors

Re: [caret-users] Open Spec File Problem

2014-12-03 Thread Donna Dierker
file is Human.PALS_B12.B1-12.DEPTH_ANALYSES_LEFT.73730.spec, which is included with the software. I have uploaded the file as Human.PALS.LEFT.zip. Thanks, Catherine On Wednesday, December 3, 2014 8:58 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Catherine, What caret

Re: [caret-users] Open Spec File Problem

2014-12-03 Thread Donna Dierker
On Wednesday, December 3, 2014 9:50 AM, Donna Dierker do...@brainvis.wustl.edu wrote: I was able to open the spec file you uploaded with no problem. There are no volume files and not that many surface files, so I doubt memory is an issue. I don't know why it is hanging on win7

Re: [caret-users] metric user scale with fixed step size

2014-11-26 Thread Donna Dierker
Hi Caspar, If you converted from Freesurfer, rather than mapping independently in Caret, then this is puzzling. I believe mris_convert can now convert directly to GIFTI (.gii) format, and I suspect this route might be more reliable than converting .w to .metric. Have you tried this?

Re: [caret-users] metric user scale with fixed step size

2014-11-24 Thread Donna Dierker
I think you should be able to write a palette like that: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile The palette file format was originally intended to be compatible with AFNI, which may have palette editing capabilities of which I am

Re: [caret-users] blacking out subcortical regions

2014-11-10 Thread Donna Dierker
There is a paint file that comes with many of the PALS-B12 datasets (e.g., Sept 2006 tutorial) that has a medial wall column. Use that as the primary overlay with your metric or other overlay as the secondary overlay. This grays out the medial wall. On Nov 9, 2014, at 10:43 AM, Frédéric

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-05 Thread Donna Dierker
. Kind regards, Rikkert On Tue, Nov 4, 2014 at 11:09 PM, Donna Dierker do...@brainvis.wustl.edu wrote: I doubt you'll be able to convert the deformation map to Caret, but it won't be necessary, if Spherical Demons can resample what you need onto the source or target mesh, after

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-04 Thread Donna Dierker
for the fiducial and inflated surfaces). Are some files missing or do I do something wrong? Thanks and kind regards, Rikkert On Fri, Oct 31, 2014 at 4:27 PM, Donna Dierker do...@brainvis.wustl.edu wrote: On Oct 30, 2014, at 11:29 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-11-04 Thread Donna Dierker
way to go? Kind regards, Rikkert On Tue, Nov 4, 2014 at 5:54 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Try this one: http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/PALS_B12/Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.borderproj login pub password download

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-10-31 Thread Donna Dierker
. If not far enough, then it's possible the McLaren atlas mesh is in register with F99. I can't recall clearly, but read that link above for more info. Thanks a lot Donna, and kind regards, Rikkert On Thu, Oct 30, 2014 at 3:13 PM, Donna Dierker do...@brainvis.wustl.edu

Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas

2014-10-30 Thread Donna Dierker
On Oct 29, 2014, at 10:56 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu wrote: Dear all, I have an averaged T1-image and co-registered volumetric atlas of the macaque brain (which has been digitized by a collaborator) and want to derive from it a surface-based atlas. Subsequently, I

Re: [caret-users] threshold of metric file

2014-10-30 Thread Donna Dierker
? Thanks! Zhiwei At 2014-10-30 00:27:14, Donna Dierker do...@brainvis.wustl.edu wrote: Hi wangzhiwei, I'm a little confused by the question. There mention of area size and scales hints that there might be a confusion between tools used for quantification / significance testing

Re: [caret-users] threshold of metric file

2014-10-29 Thread Donna Dierker
Hi wangzhiwei, I'm a little confused by the question. There mention of area size and scales hints that there might be a confusion between tools used for quantification / significance testing and those used for display purposes. Freesurfer has its own tools for significance testing, so you

Re: [caret-users] Hi res recon

2014-10-14 Thread Donna Dierker
Hi Aditya, On monkeys, yes. Humans, no. The SureFit algorithm that is in Caret's segmentation feature was designed for cubic 1mm human data. It worked reasonably well on higher res monkey data, but some of the subroutines will likely break on higher res human data (e.g., disconnecting eye,

Re: [caret-users] average fs_LR32k mesh

2014-10-01 Thread Donna Dierker
If you have individual func.gii files, then it makes sense to view them on your individual's midthickness surface. If you have group data, you might use an atlas dataset as your viewing substrate. It doesn't look like there are any 32k versions of Conte69 available for caret5 format:

Re: [caret-users] projecting functional MRI to gii surfaces

2014-09-28 Thread Donna Dierker
...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Thursday, August 28, 2014 3:47 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, There are lots of ways to split up the brain

Re: [caret-users] Different color for displaying two T-images

2014-09-23 Thread Donna Dierker
Hi Yu, I juse checked, and you can have only one palette at a time, even though you can have multiple metric overlays. When you tweak metric settings, it affects all metric overlays (at least the palette). There is a way to channel up to three metrics into a RGB map (Attributes: Metric:

[caret-users] Fwd: [HCP-Users] HCP Pipelines v3.4.0 Released

2014-09-12 Thread Donna Dierker
Begin forwarded message: From: Jennifer Elam el...@pcg.wustl.edu Subject: [HCP-Users] HCP Pipelines v3.4.0 Released Date: September 10, 2014 5:31:47 PM CDT To: hcp-us...@humanconnectome.org, hcp-annou...@humanconnectome.org Cc: f...@jiscmail.ac.uk, freesur...@nmr.mgh.harvard.edu News from

Re: [caret-users] projecting functional MRI to gii surfaces

2014-08-28 Thread Donna Dierker
. From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Wednesday, August 13, 2014 2:27 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces

Re: [caret-users] Niftii integers and PHT00 atlas acronyms

2014-08-21 Thread Donna Dierker
Try saving the paint volume as wunil ifh format. Then read the resulting .ifh file (a text file). The integer : label mappings are there, but there is a translation of two, if I recall correctly. You could also convert the surface paint file to text and look just after the header; that

Re: [caret-users] projecting functional MRI to gii surfaces

2014-08-13 Thread Donna Dierker
of Donna Dierker [do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 9:14 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces I'm not clear on what you mean by I want get fMRI time course for surface vertices

Re: [caret-users] projecting functional MRI to gii surfaces

2014-08-13 Thread Donna Dierker
...@mst.edu] Sent: Tuesday, August 12, 2014 7:16 PM To: Caret, SureFit, and SuMS software users; Donna Dierker Subject: Re: [caret-users] projecting functional MRI to gii surfaces -spec-file-change-resolution will not get you to the fs_LR 32k atlas from fs_LR 164k (but it may get you deceptively

Re: [caret-users] projecting functional MRI to gii surfaces

2014-08-06 Thread Donna Dierker
From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Tuesday, August 05, 2014 10:26 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re

Re: [caret-users] projecting functional MRI to gii surfaces

2014-08-05 Thread Donna Dierker
...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 5:34 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Push

[caret-users] Metric file must be provided for the metric mapping

2014-08-05 Thread Donna Dierker
Yesterday, I ran into two arcane issues worth passing on, one of which was covered in an earlier thread: 1. First I tried mapping a paint volume onto an atlas surface, but it turned out the volume was scalar values -- not discrete integers as I'd expected for a label/ROI volume. Caret

Re: [caret-users] projecting functional MRI to gii surfaces

2014-08-01 Thread Donna Dierker
Hi Yan, Could you use a terminal window or file manager to check whether the file exists, and if so, what its size is. We have seen cases before where the file was just a header -- no data. Inexplicably, the presence of a non-english character set on the system used has caused this sort of

Re: [caret-users] projecting functional MRI to gii surfaces

2014-08-01 Thread Donna Dierker
of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 10:10 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, Could you use a terminal window or file manager to check whether

Re: [caret-users] How to load my own file by caret?

2014-07-22 Thread Donna Dierker
of the format of *.nii.gz. Now, I want to register the result to F99 volume. But caret seems to have a very different file format, I don't know which fle set as reference in registration. ChrisTang tangzhenc...@fingerpass.net.cn Donna Dierker ?? 2014-07-21 23:34

Re: [caret-users] Issue with displaying voxel intensities

2014-06-19 Thread Donna Dierker
... Kind regards, Rikkert On Wed, Jun 18, 2014 at 8:30 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Rickert, Assuming you used File: Open Data File: type = Volume Anatomy File, you should see a normal T1w image. If you see solid white, then please upload the volume here

Re: [caret-users] MGH (label file) to caret

2014-06-19 Thread Donna Dierker
Hi Alexander, I know mris_convert can convert Freesurfer surfaces to GIFTI gii format; I think it can do the same with surfaces. The nice thing about GIFTI is that both caret5 and workbench (wb_view) can read GIFTI files. Donna On Jun 19, 2014, at 11:26 AM, Alexander Walther

Re: [caret-users] Issue with displaying voxel intensities

2014-06-18 Thread Donna Dierker
Hi Rickert, Assuming you used File: Open Data File: type = Volume Anatomy File, you should see a normal T1w image. If you see solid white, then please upload the volume here, so we can try to replicate the problem: http://pulvinar.wustl.edu/cgi-bin/upload.cgi Donna On Jun 18, 2014, at

Re: [caret-users] caret -smooth gives NaNs or values close to zero

2014-05-31 Thread Donna Dierker
Are you sure the coord, topo, and metric files all match (i.e., not only that they have the same number of vertices, but also that those vertices are in register with one another across data types)? On May 31, 2014, at 9:28 AM, Alexander Walther awaltherm...@gmail.com wrote: hi caret users,

Re: [caret-users] displaying brodmann areas

2014-05-20 Thread Donna Dierker
Hi Gabriel, More detail on how you created surfaces from my own template might help here, but let me extrapolate and provide information that might be relevant. I assume you want the Brodmann parcellation in the form of surface-based paint/label or border form (i.e., the kind of thing shown in

Re: [caret-users] mapping ALE on surface: error for number of nodes

2014-05-08 Thread Donna Dierker
Université de Montréal On Wed, May 7, 2014 at 11:30 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Another thought occurred to me: If you select a 32k version of the Conte69 atlas as your spec file, then you'll get an error when you try to open the 164k vertex metric file. I'm sure

Re: [caret-users] mapping ALE on surface: error for number of nodes

2014-05-07 Thread Donna Dierker
? In this way, we may find a way to solve the issue faster. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Tue, May 6, 2014 at 9:50 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Audrey, I will look at this more closely later

Re: [caret-users] mapping ALE on surface: error for number of nodes

2014-05-07 Thread Donna Dierker
, if you want to map directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in caret5. On May 7, 2014, at 9:58 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey-Anne, Erin and I tried to do that, but you can't see the menu picks very clearly in the video

Re: [caret-users] mapping ALE on surface: error for number of nodes

2014-05-07 Thread Donna Dierker
] mapping ALE on surface: error for number of nodes Hi, My volume is in Tal space. Is this a problem? Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 11:30 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Another thought occurred

Re: [caret-users] mapping ALE on surface: error for number of nodes

2014-05-06 Thread Donna Dierker
my data on it Can you see if I did something wrong? Thanks very much Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, Apr 30, 2014 at 3:22 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Audrey, Hmmm. I wonder if this might be because

Re: [caret-users] mapping ALE on surface: error for number of nodes

2014-04-30 Thread Donna Dierker
Hi Audrey, Hmmm. I wonder if this might be because the spec file you name below is part of the Caret distribution, and it might be read-only. In fact, it's a good idea for it to be read-only. The files under data_files are intended to be used by Caret without risk of users writing their

Re: [caret-users] how to specify palette using caret_command?

2014-04-08 Thread Donna Dierker
Hi Daniel, The palette isn't used in the mapping step (caret_command -volume-map-to-surface or -volume-map-to-surface-pals). Rather, it is used when visualizing the results of mapping (output metric), either interactively in caret5 or using a ready-made scene or caret_command -show-scene.

Re: [caret-users] p-value color bar in the surface mapping?

2014-04-08 Thread Donna Dierker
with metric? I want to show something like p .05 ~ .0001 for example. Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 4/8/14 2:19 PM, Donna Dierker do

Re: [caret-users] mapping fMRI data to surface

2014-03-31 Thread Donna Dierker
-Original Message- From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker Sent: Friday, March 28, 2014 5:07 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] mapping fMRI data to surface Do you

Re: [caret-users] mapping fMRI data to surface

2014-03-31 Thread Donna Dierker
Message- From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker Sent: Monday, March 31, 2014 11:07 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] mapping fMRI data to surface Hi Hu, No, there's

Re: [caret-users] mapping fMRI data to surface

2014-03-31 Thread Donna Dierker
(maybe it's due to the normalization in SPM). Regards, Hu -Original Message- From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker Sent: Monday, March 31, 2014 12:18 PM To: Caret, SureFit, and SuMS software

Re: [caret-users] mapping fMRI data to surface

2014-03-28 Thread Donna Dierker
Do you have a non-English character set installed on this computer? We have had issues with writing metric files when a non-English character set was installed, but the error I recall was worded slightly different. On Mar 28, 2014, at 1:22 PM, Cheng, Hu wrote: Dear Caret users, I'm

Re: [caret-users] volume data corresponding to the MNI surface data

2014-03-21 Thread Donna Dierker
by Copy Surface Paint Column to Paint Volume, but I need to select the volume space. So I hope you could give me some advice on the selection. Cheers, Zhuangming Shen -原始邮件- 发件人: Donna Dierker do...@brainvis.wustl.edu 发送时间: 2014年3月20日 星期四 收件人: Caret, SureFit

Re: [caret-users] volume data corresponding to the MNI surface data

2014-03-20 Thread Donna Dierker
. By the way, which space (AFNI, FLIRT, FLIRT-222, FNIRT, FNIRT-222, MRITOTAL, SPM, SPM95, SPM96, SPM2, SPM5, T88, 711-2B, 711-2C, 711-2O, 711-2Y) should I choose for mni_icbm152_t1_tal_nlin_sym_09a.nii ? Thanks again! Cheers, Zhuangming -原始邮件- 发件人: Donna Dierker do

Re: [caret-users] Distorted COMPMEDWALL

2014-02-18 Thread Donna Dierker
no.503-614-3755 Mob No.-503-799-7204 On Thu, Feb 13, 2014 at 9:02 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Ahmad, Even if your anatomical volume is in LPI orientation, I don't think your surface is. Does the segmentation volume used to generate that surface align properly

Re: [caret-users] Distorted COMPMEDWALL

2014-02-12 Thread Donna Dierker
Research Center (ONPRC) Oregon Health and Science University (OSHU),Portland Oregon- 97006 Ph no.503-614-3755 Mob No.-503-799-7204 On Thu, Jan 16, 2014 at 5:42 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: When I see something like that, I wonder if your fiducial surface

Re: [caret-users] Visualization in Caret

2014-02-08 Thread Donna Dierker
hemisphere). Thank you, Eshita On Fri, Feb 7, 2014 at 1:13 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Maybe I am the one who is mistaken, but I thought this is how these columns behaved. I would be more than happy to look at your *significan*metric if you want to upload

Re: [caret-users] Errors in Stage-3.FS-to-F99.sh: Expected '' or '/', but got '[0-9]'

2014-02-07 Thread Donna Dierker
I checked, and there was some off-list exchange between me and the poster, but it didn't address this error, per se. The solution for this user was to use mri_convert to reorient rawavg.mgz, which was in sphinx orientation, the translate per

Re: [caret-users] Visualization in Caret

2014-02-07 Thread Donna Dierker
threshold to be 0.05. Is there anything else in my settings that may be contributing to this error? I have 35 controls and 60 treatment subjects. I am looking into running the two-sample t-test instead of anova. Thanks for your help! Eshita On Wed, Feb 5, 2014 at 3:54 PM, Donna Dierker

Re: [caret-users] Visualization in Caret

2014-02-05 Thread Donna Dierker
AM, Donna Dierker do...@brainvis.wustl.edu wrote: Yes, pretty much: I usually have a study directory into which I copy the Conte69 files. Then I rename the Conte69 spec to something more study-specific. I usually use the Conte69 inflated and very inflated for t-map visualization, along

Re: [caret-users] display myelin mapping results

2014-02-05 Thread Donna Dierker
From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Thursday, January 30, 2014 11:22 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] display myelin mapping results

Re: [caret-users] display myelin mapping results

2014-02-05 Thread Donna Dierker
repeat the procedures on your data? Hu From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Wednesday, February 05, 2014 9:42 AM To: Caret, SureFit

Re: [caret-users] Visualization in Caret

2014-02-05 Thread Donna Dierker
groups and want to see where one group is deeper than the other, you can run a t-test instead of an anova. Thanks for your help, Eshita On Wed, Feb 5, 2014 at 5:58 AM, Donna Dierker donna.dier...@sbcglobal.net wrote: Use the D/C: Metric Settings menu to adjust the threshold to .90

Re: [caret-users] Visualization in Caret

2014-02-03 Thread Donna Dierker
of information right below the header, as you mentioned. But for the TFCE report, I don't see anything similar. Maybe I am interpreting it incorrectly? Thank you, Eshita On Fri, Jan 31, 2014 at 1:15 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: On Jan 31, 2014, at 2:17 PM

Re: [caret-users] Freesurfer to F99 without volume?

2014-01-31 Thread Donna Dierker
I assume you mean this tutorial: FS-to-F99_Tutorial_Sept10.doc http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8285962 I confess I'm not as familiar with the details of that one, but my hunch is that the volume is being used here not to drive registration directly, in the way it would a

Re: [caret-users] Visualization in Caret

2014-01-31 Thread Donna Dierker
On Thu, Jan 30, 2014 at 5:17 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: Wow, does this mean you got past the grind-to-a-halt JRE problem? Excellent! Here is a script I used to compute mean midthickness surfaces for two groups: http://brainmap.wustl.edu/pub/donna/US/UCLA

Re: [caret-users] display myelin mapping results

2014-01-30 Thread Donna Dierker
copy their spec file and replace all the files? Thank you very much! Regards, Hu -Original Message- From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker Sent: Monday, January 20, 2014 6:18 PM To: Caret

Re: [caret-users] Visualization in Caret

2014-01-30 Thread Donna Dierker
Wow, does this mean you got past the grind-to-a-halt JRE problem? Excellent! Here is a script I used to compute mean midthickness surfaces for two groups: http://brainmap.wustl.edu/pub/donna/US/UCLA/ESHITA/gen_mean_fiducials.pared.sh login pub password download But the main command is this

Re: [caret-users] Create Foci

2014-01-29 Thread Donna Dierker
Can you upload your cdv file here (just one of them): http://pulvinar.wustl.edu/cgi-bin/upload.cgi And tell us which atlas/tutorial you were using for mapping the foci (e.g., PALS or Conte69)? On Jan 28, 2014, at 3:43 PM, Lauri lort...@yahoo.com wrote: Dear caret-users, I am trying to

Re: [caret-users] display myelin mapping results

2014-01-29 Thread Donna Dierker
-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker Sent: Monday, January 20, 2014 6:18 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] only got one hemisphere from surefit SureFit only segments one hemisphere at a time. You need to crop to a left or right

Re: [caret-users] Using caret_stats for TFCE

2014-01-23 Thread Donna Dierker
can send you. On Jan 22, 2014, at 4:27 PM, Eshita Shah eshs...@ucla.edu wrote: Yes, it works fine at 1000 iterations. I am trying to run 5000. It seems to get really slow after 1000, but continues on to about 2600 until it crashes. On Wed, Jan 22, 2014 at 2:13 PM, Donna Dierker do

Re: [caret-users] Using caret_stats for TFCE

2014-01-22 Thread Donna Dierker
just downloaded the JRE you provided, and it is actually the same one that I am using. Do you think there is another source of this problem? Thank you, Eshita On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: At the end of the TFCE processing

Re: [caret-users] only got one hemisphere from surefit

2014-01-20 Thread Donna Dierker
SureFit only segments one hemisphere at a time. You need to crop to a left or right hemisphere and run them separately. On Jan 20, 2014, at 3:36 PM, Cheng, Hu huch...@indiana.edu wrote: Dear Caret User, I’m running Caret on a 64-bit Windows. I tried to segment an individual’s T1w

Re: [caret-users] freesurfer to caret piepeline

2013-12-03 Thread Donna Dierker
. The new caret5 GUI works just fine. Thank you, --ts On 11/27/2013 05:18 PM, Donna Dierker wrote: Good question. You could use different versions for the two steps, but you'd have to report that in your methods, which could get messy. Running pre border.sh with the older caret_command

Re: [caret-users] Paintfiles in Native Space

2013-12-02 Thread Donna Dierker
If you have opted to run the registration both ways (individual to atlas and atlas to individual), you should be able to get the atlas goodies on the native mesh. If they were not in the spec file when you ran the registration, then you can apply the deformation map in the native directory to

Re: [caret-users] unable to choose Map To Spec File with Atlas

2013-11-28 Thread Donna Dierker
I have a suspicion: Somehow, you could have gotten a link/shortcut/caret5-binary-itself on your desktop or some other location that is displaced from the rest of the caret distribution. (This happened to me recently, which is why it comes to mind.) In order for caret to see the atlas spec

Re: [caret-users] freesurfer to caret piepeline

2013-11-27 Thread Donna Dierker
, although with 144 cycles. Are you saying we should switch back to the old caret for the time being? I mean, the check_reg result seems fine, but maybe there's still something wrong with it? Thank you! --ts On 11/27/2013 11:27 AM, Donna Dierker wrote: Hi Taosheng, I tried running

Re: [caret-users] freesurfer to caret piepeline

2013-11-27 Thread Donna Dierker
and it does finish, although with 144 cycles. Are you saying we should switch back to the old caret for the time being? I mean, the check_reg result seems fine, but maybe there's still something wrong with it? Thank you! --ts On 11/27/2013 11:27 AM, Donna Dierker wrote: Hi Taosheng

Re: [caret-users] Try #2

2013-11-23 Thread Donna Dierker
different between the two groups after statistical analysis. Thank you, Eshita On Thu, Nov 21, 2013 at 4:33 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: I would use the Conte69 for TFCE/cluster area computation purposes. Think of it as a neutral, unbiased atlas surface

Re: [caret-users] Try #2

2013-11-21 Thread Donna Dierker
curious as to whether I should just generate my own average fiducial file and use that instead. Let me know if I'm heading the right way. Thanks for all your help, Eshita On Tue, Nov 19, 2013 at 2:35 PM, Donna Dierker do...@brainvis.wustl.edu wrote: Here are the caret_stats and jre

Re: [caret-users] Try #2

2013-11-19 Thread Donna Dierker
the open topo file, but to input into ANOVA should I be creating an average topo file of all my subjects? Please let me know. Thank you for your patience and help. Eshita On Fri, Nov 15, 2013 at 3:50 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: Scroll down eshita From

Re: [caret-users] Different Node Numbers

2013-11-15 Thread Donna Dierker
-surface-average to generate an average fiducial file for each hemisphere. Is this correct? Please let me know. Thanks, Eshita On Wed, Nov 13, 2013 at 10:50 PM. Donna Dierker wrote: Hi Eshita, I always use the open topology for this purpose (i.e., excludes only medial wall vertices

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