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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
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Hi Ziad,
Thank you very much. I updated afni, and it worked
Thanks,
Mahshid
by
Mahshid
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AFNI Message Board
Hi SUMAs,
I ran @SUMA_Make_Spec_FS and it successfully makes Subj_both.spec,Subj_lh.spec,Subj_rh.spec and *_SurfVol+orig files. But it fails in MapIcosahderon and cannot make std.141 and 60. The error I received is:
Running MapIcosahedron for both hemispheres at ld values of 141 60
++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:789 @01:23:33):
Adding -NN_dset_map ./lh.aparc.a2009s.an
by
Mahshid
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AFNI Message Board
Hi Ziad,
Sorry for late response, I just see your comment now. Yes I am sure, it is fast maybe because I use teamviewer(?) or maybe because both computers are using campus Internet so it becomes like local connection(?)..
by
Mahshid
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AFNI Message Board
Hi Rick,
You are right, the grayordinate format is in NIFTI-2 format, since the output is:
n + 2 \0 \r \n 032 \n
I wish AFNI could support it now,,but, Isn't there any way like "ConvertDset" or anything else which can convert the NIFTI-2 format to the niml or 1D format (like what we use in suma)?
About the volumetric data, the 3dinfo output is:
Dataset File:
by
Mahshid
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AFNI Message Board
Thank you, 3dcopy worked for the volumetric data but not for the grayordinate timeseries.
It gives following errors:
3dcopy rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii test1
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jan 8 2014) [64-bit]
*+ WARNING: missing view dataset: rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii+orig - SKIPPING
*+ WARNING: missing view dataset: rfMRI_REST2_RL
by
Mahshid
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AFNI Message Board
Dear AFNIs,
Hi,
I plan to use Human connectome data, which provides both in volumetric and surface (grayordinate) timeseries files. Both files have .nii suffix.
When I use afni codes such as 3dFourier as follows, I receive following error for the surface data:
3dFourier -lowpass .08 -retrend -prefix test.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii
++ 3dFourier: AFNI version=AFNI_2
by
Mahshid
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AFNI Message Board
Hi again,
Problem Solved:
I gave the node index as the input for the ROIgrow (in matlab using something like find(isodist.ext.1D.dset~=0)-1 and give it to ROIgrow) not the isodist.ext.1D itself, which includes nonzero values for the centers.
Thanks Ziad for your help,
Mahshid
by
Mahshid
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AFNI Message Board
Not actually. When I only display one of them it is OK, but there is a problem, the ROIs centers are not according to the centers in the isodist.ext.1D, just a few of them, and so the results have overlap, and do not cover whole brain. Actually it covers only a very small part of brain (attached the images). left: isodist.ext, right bottom: only 1 output of ROIgrow, right top: the overlap of all
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Mahshid
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AFNI Message Board
I use teamviewer to access remotely:
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
++ Notice SUMA_F12_Key (SUMA_input.c:1025 @12:35:57):
Elapsed time: 0.267758 seconds.
74.69 displays/second.
In Polymode 1, rendered
1075.60 Ktri/sec 537.81 Kpnt/sec.
by
Mahshid
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AFNI Message Board
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 not contain only 1s, but 1 to 476, so in next step ROIgrow made 476 seprate files, but easily I loaded isodist.ext.1D.dset in Matlab and c
by
Mahshid
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AFNI Message Board
Hi,
I want to define surface-based ROIs which distribute uniformly spaced (let's say about 15mm) apart on the whole surface (perferably consist of one vertex, but it is OK as long as they do not have overlap or their space from boundaries are the same, too). I tried ROIgrow, but the output results are not uniformly seprated. Could you please let me know how it can be done?
Thank you,
by
Mahshid
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AFNI Message Board
Hi,
I want to run some surface analysis on resting state data. So, First I used Freesurfer to extract the surfaces and applied SUMA on them, having standard meshes ready. Also I did common functional data preprocessing steps, and finally used 3dVol2surf and Surfsmooth to smooth the data as follows:
3dVol2Surf \
-spec ${S
by
Mahshid
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AFNI Message Board