Show all posts by user
Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely,
AFNI HQ
History of AFNI updates
Hi PT,
You're missing libpng it seems. Is it no longer in fink?
z
by
ziad
-
AFNI Message Board
Hi Linda,
What do you mean by you can't open it? Does it not load into SUMA? That is the simplest way to look at it. You can use 3dinfo on the dataset to get some information about sub-brick labels etc. But you really should be looking at your results before you push them all into the the group analysis phase.
z
by
ziad
-
AFNI Message Board
Hi Beau,
You need to use the option -num_stimts before you specify any -stim* options. See 3dDeconvole -help (or -h_view) for details.
cheers
Ziad
by
ziad
-
AFNI Message Board
Hello Josh,
Well, the design may be sub-optimal in that the response to cigarette is considerably correlated with that of the neutral cues. You should examine your design matrix to find out how correlated the two stimulus response models are. The more correlated two responses are the more data one needs to tell them apart. The program ExamineXmat can help you check on the amount of correlation
by
ziad
-
AFNI Message Board
Hi Linda
> If I can use the" 3dcalc" to calculate the
> subject.niml.dset file, so that I can get mean
> value at each node from a group of subjects.
> Is it right to use it as followed:
> 3dcalc -a Subject1.niml.dset[6] \
> -b Subject2.niml.dset[6] \
> .
> .
> .
> -expr mean(
by
ziad
-
AFNI Message Board
Hi Peter,
>
> Oddly specific enquiry: Is it possible to create a
> surface ROI (e.g. lh.xxx.niml.roi) from a surface
> dataset (e.g. lh.data.niml.dset) the same way you
> would use 3dcalc to generate a binary mask in
> volume space? In other words, is it possible to
> generate a surface ROI automatically, instead of
> drawing it, or somehow convert a surface datas
by
ziad
-
AFNI Message Board
Hi Linda,
You're right about why ScaleToMap is giving you different colors for the same value. However, I don't think you need to use ScaleToMap at all. Usually we colorize data directly and interactively in suma. Have you tried this at all? You would load each hemisphere's dataset onto its corresonding surface and then colorize the data interactively using the SurfaceController
by
ziad
-
AFNI Message Board
Hello,
I suspect there are typos in the file extensions you are reporting. You should be getting .1D.dset or .niml.dset from 3dVol2Surf. Of the two, I highly recommend you use the .niml.dset, which you get by using the option -out_niml in 3dVol2Surf. I also recommend you use the option -oob_value 0 .
The .niml.dset files can be read directly by 3dttest. There is no need for translation.
c
by
ziad
-
AFNI Message Board
Hi Ryan,
I am not sure what is wrong with the 3drefit command, I might need to take a look using your dataset. But before we go down this route, did you try the -dset option in SurfToSurf ? This should allow you to create niml dataset instead of the.1D that you got with the -data option.
cheers,
Ziad
by
ziad
-
AFNI Message Board
Linda Wrote:
-------------------------------------------------------
> For anatomical data: I get the result from the
> freesurfer and translate the result by using
> @SUMA_Make_Spec_FS and then MapIcosahedron.
The new @SUMA_Make_Spec_FS will run MapIcosahedron for you. I also recommend the -GIFTI option which creates more convenient output.
> For functional data: I do the
by
ziad
-
AFNI Message Board
The simplest is to create your own, just make a copy of the one from the demo and modify it to fit your surfaces.
cheers,
Ziad
by
ziad
-
AFNI Message Board
Hi Nick,
This is certainly possible, but not having touched ToyTalk in ages, I am not actually sure how reliable it still is.
At the moment, the ToyTalk implementation is mostly matlab code that duplicates some of what is done in the C-api that AFNI/SUMA use. I am wondering if we should make the effort to start using the same API from matlab and/or from Python. Otherwise it will be too much
by
ziad
-
AFNI Message Board
(From an earlier email reply)
Hello Yufeng,
Dear Sir,
I want to translate the freesurfer result to the AFNI by using SUMA. Now I want all the subjects to align to a Standard-Mesh Surfaces. My question is as followed:
1. If I need to use MapIcosahedron to produce the Standard-Mesh Surfaces for every subject or the @SUMA_Make_Spec_FS now generates standard-mesh surfaces by default.
You
by
ziad
-
AFNI Message Board
Hello John,
I just want to add to Daniel's suggestions that you should avoid using the integers directly because the integer<-->name mapping can change with newer versions and you might be in for a world of pain. So in the commands above, better substitute the area numbers with their respective names.
cheers,
Ziad
by
ziad
-
AFNI Message Board
Do you get the help output from:
3dMVM -help
Also, in the same directory where you are running the commands and getting the error, what does the following command yield?
ls -la | grep MVM
by
ziad
-
AFNI Message Board
Hi 3dFoodie,
Try updating first with this:
@update.afni.binaries -package macosx_10.7_Intel_64
then try again.
I suspect that would solve the problem.
cheers,
z
by
ziad
-
AFNI Message Board
Where is the b0 image in the 4d DWI volume? If it is the nth volume in the 4D array (we start counting at 0), then what you want is:
3dcalc -a original.nii'' -expr 'a' -prefix your_nth_volume
The example you are suggesting from FSL seems geared for extracting values in a certain range. There is another syntax for that of course. Consider the output of 3dcalc -help, or -h
by
ziad
-
AFNI Message Board
Hi Jason,
I'll compliment Nick's reply with some historical perspective. Way back when we developed MapIcosahedron, we used ld141 because the vast majority of edges were smaller than those of the densest surfaces we used, those from FreeSurfer. So, the idea there is to preserve any detail present in the original meshes. To get information about the mesh you are viewing in suma, open
by
ziad
-
AFNI Message Board
Hello Taka,
I have not read the paper but in terms of segmentation, 3dSeg would give you posterior prob. estimates for the three classes. If you are more specific about how you want to use them I might be able to point you to other programs that can help you do what you want.
cheers,
Ziad
by
ziad
-
AFNI Message Board
Hi Naveed,
So what are the 3dANOVA2 files that get written out? Do they end with .niml.dset?
Viewing them should be straight forward.
1- Open suma with one set of standard meshes that matches the one you used for the analysis
2- Select one hemisphere (right-click), open the surface controller (view --> Surface Controller, or ctrl+s) then click on "Load Dset" and pick the datas
by
ziad
-
AFNI Message Board
Hi Oori,
I have not pondered this before, though I do have a program (SurfExtrema) that computes the gradient on the surface. You might be able to use it to create the distributions you mentioned.
cheers,
Ziad
by
ziad
-
AFNI Message Board
Hi Nick,
The problem was caused by a recent change I had made in an effort to save some CPU time under certain conditions. I will check the repair in sometime tomorrow and binaries should be rear to go tomorrow (Tuesday March 4th) evening. If you want binaries before then, send me an email with the binaries version you need and I'll make some available to you earlier.
cheers.
z
by
ziad
-
AFNI Message Board
Oops, I am the most likely culprit. There is always excitement when I mess with I/O functions…
I will consider and report back.
cheers,
z
by
ziad
-
AFNI Message Board
Hello superbug,
That's funny looking stuff to be sure. Let's try a thing or two before asking you to send me data to reproduce this.
Try rerunning the command from the directory where the output for subject 003 resides:
so cd …../003
when you're there an ls command should show you FreeSurfer directories such as orig/ mri/ surf/, etc.
then run:
@SUMA_Make_Spec_FS -GIFTI -
by
ziad
-
AFNI Message Board
Hi Kara,
Any smoothing would be done on the surface so even with retinotopy it should be OK. If you want to see the effects of smoothing on retinotopic data, consider the demo material available with: @Install_AfniRetinoDemo.
Otherwise, the command looks good, go for it!
cheers,
z
by
ziad
-
AFNI Message Board
Hello,
It looks like 3dStatClust might do what you want, but 3dmerge won't. I say might because I have never used the program myself and it looks like it does not like to read in .1D files (or surface datasets for that matter). I can look into adding this functionality but I cannot get to it for a while longer. Would you still care for it in a couple of weeks?
cheers,
z
by
ziad
-
AFNI Message Board