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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 Kara,
I think you're still not using the standard mesh surfaces in the afni_proc.py command. What is the exact afni_proc.py command you used to process the data on the surface? The -surf_spec option should be specifying one of the standard mesh spec files, not the original ones. So for example, you'll need to use
-surf_spec std.120.YOUR_SUBJECT_ID_lh.spec
instead o
by
ziad
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AFNI Message Board
Hi Melanie,
It is a notice, not an error, are you getting proper output? I'll mute that message for future releases.
cheers,
Ziad
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ziad
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AFNI Message Board
Hi Kara,
Nick's suggestions are spot on but there might be a bug with ConvertDset for that particular command you are running. I am not sure what is causing the errors you got with ConvertDset. I am on vacation until Tuesday so I can't look into it much before then.
For the moment, it might be easiest that you rerun at least one of your afni_proc.py commands with the added regre
by
ziad
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AFNI Message Board
Hi Justin,
3dSeg does get an estimate of the bias field, so you might want to give it the original data. But if the bias is too strong, you may be better off passing the 3dunifize output as long as you have non-brain areas masked.
cheers,
z
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ziad
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AFNI Message Board
Hi Jen,
In addition to Rick's recommendation, I should mention that usually you need not map smoothed time series back to the volume. Most 3d* programs, the ones that do not involve inter-voxel operations (like 3dclust, or 3dmerge -1blur*), will work on surface-based data.
Also, if you are just mapping meridia in this experiment, it might be easier to use linear regression with 3dDeconvo
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ziad
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AFNI Message Board
Hi Kara,
Those scripts are for rotating wedges and expanding rings. In your case, I suspect it is best to process the data with linear regression using as many stimulus classes as you have discrete stimulus positions (2 or 4?). From this you can create maps showing the responses to each of the meridia and then draw the boundaries accordingly.
It would be best to use afni_proc.py to perform t
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ziad
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AFNI Message Board
Hi Jie,
Something is fishy with the results of the right hemisphere, it seems. Can you send me the output stats for both left and right hemis, and tell me which icosahedron mesh you used (-ld parameter)?
If the files are too big and you need uploading instructions send me an email and I'll reply with the information.
cheers
z
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ziad
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AFNI Message Board
Hi Mahshid,
That is faster than what I get rendering locally!
Just to be sure, I assume you also used "suma -i ld120" &, correct?
cheers,
z
by
ziad
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AFNI Message Board
That should not be the case, though we should start by defining what you mean by native space. The -GIFTI option should result in a volume that is in the same space as what you passed to FreeSurfer. If that is not the case then I will need to take a look at the case you have. For that I would need you to send me the output of the FreeSurfer run for that subject. If you want to try this route send
by
ziad
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AFNI Message Board
Hi,
Try again but add the option -GIFTI with @SUMA_Make_Spec_FS and you should get the results in the native space.
Let me know if that works out for you or I can look into this further.
cheers,
Ziad
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ziad
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AFNI Message Board
Hi Aimi,
I don't know what it casing this problem so the best approach is to contact the Neurodebian folks about it.
cheers,
z
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ziad
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AFNI Message Board
chxc123 Wrote:
-------------------------------------------------------
> Hi Ziad,
>
> Thanks for your suggestion.
>
> I tried it and loaded the output file onto a
> inflated std.141 surface. It looked like a mesh
> covering the brain surface, but the locations and
> size of BA areas looked fine.
>
Do you mean the color pattern covered the whole surface? Wha
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ziad
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AFNI Message Board
Hi Isaac,
This should be fixed in future versions. Thanks for bringing it up.
cheers,
z
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ziad
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AFNI Message Board
OK,
Can you rerun the @SUMA_Make_Spec_FS command but add the option -GIFTI ?
Is the result any different with the new option?
If you are still having a bad alignment, I will need you to upload the entire FreeSurfer directory for that subject because I will need to run the @SUMA_Make_Spec_FS command locally to debug this.
Send me an email if you need instructions for uploading an arch
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ziad
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AFNI Message Board
Hi Xiangchuan,
You can make use of the node mapping file created by MapIcosahedron (via @SUMA_Make_Spec_FS). That would greatly speed up the last step. See 'NOTE II' in the help output of MapIcosahedron.
If you need more help, let me know.
cheers,
z
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ziad
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AFNI Message Board
Hi Jennifer,
What is the exact pair of SUMA and AFNI commands you ran that led to the bad alignment?
If you used for -sv the volume that you passed to FreeSurfer, rather than the one created in the SUMA/ directory by @SUMA_Make_Spec_FS then you may very well get a bad alignment.
Also, assuming you are using a recent version of AFNI/SUMA, I recommend you start using @SUMA_Make_Spec_FS with
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ziad
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AFNI Message Board
mahshid Wrote:
-------------------------------------------------------
> Hi all,
>
> Thanks very much for your helps.
>
> Ziad,
> I tried using SurfExtrema as what you said,
> SurfExtrema -i
> subj_surface/SUMA/std.141.lh.smoothwm.asc -input
> tt.1D.dset -hood 15 -thresh 0 -gthresh 0 -prefix
> isodist
>
> But the file isodist.ext.1D.dset did no
by
ziad
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AFNI Message Board
Try this for another flavor:
Say your surface is SURF and the number of nodes on your surface is: N
#Create a constant
1deval -num $nn -expr '+5' > tt.1D.dset
#Find extrema with thresholds turned off
SurfExtrema -i SURF -input tt.1D.dset -hood 15 -thresh 0 -gthresh 0 -prefix isodist
The file isodist.ext.1D.dset contains a 1 for each node that represents the center of the ROI
by
ziad
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AFNI Message Board
Hi Mahshid,
There are no tools to do this at the moment. However one way to do this is to consider a standard mesh with a low number of subdivisions. For instance, if you want about 4000 nodes over the whole hemisphere, you can create standard meshes with ld20 and then use the nodes from the low res mesh to place the seeds on the high-res surface mesh. SurfaceMetrics -closest_node_XYZ can help
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ziad
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AFNI Message Board
So for some reason the message board software is refusing to display your last response containing the result of your 'ls' command. But I had a copy emailed to me. It is strange that I do not see an mri/ directory that would contain all of the volumes like "lh.ribbon.mgz", "orig/orig.mgz", and directories such as "orig/" "transforms/" etc. You do
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ziad
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AFNI Message Board
Thanks again for the numbers, this is quite helpful.
cheers,
Ziad
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ziad
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AFNI Message Board
DOH!
Not sure what happened but the code checkout for the build was incomplete and caused major headaches down the line. I am rebuilding this instant, so good code should be back online in a couple of hours (I will post an update to be sure).
cheers,
z
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ziad
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AFNI Message Board
Hi Emily,
You might be better off using @ROI_Corr_Mat, or the program 1dCorrelate
At least you can use those alternate programs to verify what you got out of 3dim+ which has to be tortured a bit to get at what you want.
cheers,
Ziad
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ziad
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AFNI Message Board
Hi Chris,
So after GIT says it is ready if you just do 'shift+ctrl+ left click' in one of AFNI's slice windows nothing happens?
The output I get from 3dGroupInCorr right after I launch it is different from yours (see below). I get a few more lines past the thread count. The easiest thing to try is a software update followed by a new attempt. We'll see where that gets us
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ziad
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AFNI Message Board
Good info, thanks a lot.
As for the suma command, change the '-i Id120' to '-i ld120' with the 1st two characters of the surface name being lowercase L and lowercase D. This is code for SUMA to create a sphere from an icosahedron mesh that is identical to what CreateIcosahedron's -ld 120 option would have produced.
cheers
z
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ziad
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AFNI Message Board
Hello folks,
I am wondering if any of you have been running SUMA on a remote server with a somewhat decent response time. Running over ssh for example is unbearably slow. If you do have a decent setup, I would appreciate some pointers and if you could let me know what the SUMA 'F12' speed test returns when run on the SUMA rendering using this command:
suma -i ld120 &
by
ziad
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AFNI Message Board
It is possible, you can use 3dmaskdump to extract values from a volume, but you will get the whole volume in one column (or one column for each sub-brick, to be precise), so you will need to reshape the column into a matrix form. The -index option will include each voxel's i,j,k values in addition to the test results. This would make it easier for you to figure out how the output asciii for
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ziad
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AFNI Message Board