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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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Results 1 - 27 of 27
I want to get the standard deviation(SD) of single subject. I can get beta(coefficient) and T from the 3dDeconvolve.
I wonder if SD=Beta/T?
by
Linda
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AFNI Message Board
I need to calculate the distance between two points on grey matter. But the cortex consists of the grey-colored mass of folds and grooves. The distance based on the voxel in afni can not get the real distance. So I need to flatten the cortex and get the coordinate in surface-based coordinate or flattened-based coordinate.
I want to know if SUMA can give me the node coordinate in spherical-ba
by
Linda
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AFNI Message Board
1I want to know the coordinate of each node in SUMA ( after doing the @SUMA_AlignToExperiment but do not do the 3dvol2surf) based on the spherical mesh or volume-based mesh.
2I want to know the coordinate of each node in SUMA ( after doing the 3dvol2surf) based on the spherical mesh or volume-based mesh.
3 I want to know if every one's surface has been align to each other in surface or I n
by
Linda
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AFNI Message Board
Hi everyone,
I use @SUMA_AlignToExperiment first.
Then I use "afni -niml&“
ctrl+c
suma -spec subject.spec -sv sujbect_SurfVol_Alnd_Exp
t (to link volumn to surface)
And Now I can get the peak position of the stimulate response both in afni and SUMA coordinate system.
Now I want to calculate the distance
by
Linda
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AFNI Message Board
Hi everyone,
I use the @RetinoProc to do the reitnotopic mapping, but the result is not very good. So I use the 3dRetinoPhase to do it on the voxel not on the surface. The result is good.
My question: On the surface, I can use the SurfRetinoMap to add the ccw, clw, con,and exp result to get the vfr field. But now I deal with it on the voxel not on the surface. I want to know how to add the
by
Linda
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AFNI Message Board
First I use
3dDeconvolve -input sdr*.nii.gz \
-num_stimts 30 \
-polort A \
-stim_times 1 ${path}/location_1.1D 'SPMG2(0)' -stim_label 1 con1 -stim_maxlag 1 0 \
... ...
-fout \
-tout \
-bucket sm_SPMG2.nii.gz \
To point ou
by
Linda
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AFNI Message Board
I think we can the total stimulates result from -bucket file. Then use 3dcalc to get the beta for each stimulate.
And now I am not sure about the function of -iresp. If I use it use as followed:
-stim_times 1 ${path}/location_1.1D 'SPMG2(0)' -stim_label 1 con1 -stim_maxlag 1 0 \
-fout \
-tout \
by
Linda
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AFNI Message Board
>
> Would you provide a little more information about
> your stimuli and the regression step? Are
> subjects
> watching a movie or something? Is this some sort
> of
> correlation analysis?
>
> - rick
Hi rick,
My stimuli: the flashing points show up on the 24 different positions. Some of them will show up at the same time but at different positions. Eac
by
Linda
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AFNI Message Board
Thanks very much!
1 How to select the value of -polort? -1,1or A?
I am a little confuse about the -porlort option: As I want to compare the different group and they watch the same stimulate.
by
Linda
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AFNI Message Board
1 How to select the value of -polort? -1 or A?
2 I use the SPMG2 and write the code as:
-stim_times 1 ${path}/location_1.1D 'SPMG2(0)' -stim_label 1 con1 -stim_maxlag 1 0 \
Then I then the result as :
#0 Full_Fstat
#1con1#0_Coef
#2 con1#0_Tstat
#3con1#1_Coef
#4 con1#1_Tstat
#5 con1_Fstat
Which one is the beta I want?#1or #3?
by
Linda
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AFNI Message Board
Hi Ziad,
In the suma_demo, I find the Ref_10on20Off_GAM.1D for the -ideal_file is as followed:
0
0
0
8.96394
98.7984
174.641
197.894
201.986
193.529
103.695
27.8522
4.59949
0.507025
0
0
0
0
0
8.96394
98.7984
174.641
197.894
201.986
193.529
103.695
27.8522
4.59949
0.507025
0
0
0
0
0
... ....
For my stimulate, I has about 8 stimulate. And each of the last abo
by
Linda
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AFNI Message Board
I want to know how to get the file for the -ideal_file in the 3ddelay for my own data. Thanks!!
by
Linda
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AFNI Message Board
I want to know what should I do next, if I do not want tohave this kind of warning. Chang the name of the input?
I want to know if I do not need the covariate, the warning will effect on the result or not?
by
Linda
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AFNI Message Board
I have two group of subjects.For each subject. I take two scans for each subject with two condition. Then I do the 3dTcorrelation for this two scan within each one subject. So I get the correlation coefficient for each voxel for each subject. The value of the correlation coefficient is range from -1 to 1.
Now, I want to do the 3dttest++ for the two group of subjects. I want to know if I need t
by
Linda
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AFNI Message Board
I use the 3dtttest++ as followed:
3dttest++ -setA /subject1/1.niml.dset \
/subject2/1.niml.dset \
.
.
.
-setB /subject3//1.niml.dset \
/subject4//1.niml.dset \
.
.
by
Linda
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AFNI Message Board
Hi Ziad,
I am sorry that I do not explain it properly. But for the subject.niml.dset, I can not know which column contain the value I need. I can not know which column should be the input for ''3dcalc'' , '' 3dMean'' and "3dttest".
The followed is the information I get from the SurfDsetInfo and 3dinfo.
SurfDsetInfo v2s.MaskS_unsmooth_corr_mo
by
Linda
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AFNI Message Board
Dear Ziad,
I can not open the subject.niml.dset. So I am not sure which value should I use in it. As I want to get mean value at each node from a group of subjects. In the subject.1D.dat, I know the value is in the 6th column. But for the subject.niml.dset, I can not figure out what is in it. So I have no idea about how to use 3dcalc and 3dMean for it.
I want to make sure if it is right as
by
Linda
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AFNI Message Board
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(a,b,...)
-prefix mean_suject.niml.dset
I want to
by
Linda
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AFNI Message Board
Dear Ziad,
I have two groups of subjects. And I get the subject.1D.dat and subject.niml.dset for each subject by using 3dVol2surf. I want to get mean value at each node from these two groups. In the old version of suma.doc, it tells to do as followed:
1deval -a 'DataSurf_s1.1D.dat[6]'
-b 'DataSurf_s2.1D.dat[6]'
-c 'DataSurf_s3.1D.dat[6]'
by
Linda
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AFNI Message Board
Dear sir,
I get two result file ( subject.1D.dat) for two group of subjects. I want to set the same color value for the the same value in these two file. But I find the same value get the different color value in these two file after using ScaleToMap. Maybe it is because the value range is different in the two file. I want to know what should I do to set the same color value for the the same v
by
Linda
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AFNI Message Board
Dear sir,
I get two result file ( subject.1D.dat) for two group of subjects. I want to set the same color value for the the same value in these two file. But I find the same value get the different color value in these two file after using ScaleToMap. Maybe it is because the value range is different in the two file. I want to know what should I do to set the same color value for the the same
by
Linda
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AFNI Message Board
Dear Sir,
First, I use @SUMA_Make_Spec_FS to convert the anatomical data and make the standard-Mesh surfaces. The standard-Mesh surfaces node of the every subject is the same: 198811.
Then I use the @SUMA_AlignToExperiment and 3dVol2Surf to map the functional data to the surface, and then the result data file: DataSurf.1D.dat. But for few subject, there is some node lose in the DataSurf.
by
Linda
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AFNI Message Board
I find the file: Ref_10on20Off_GAM.1D as the input -ideal_file opinion for 3ddelay in the suma_demo. I want to know how to get the my own file. I can not know how to write it.
by
Linda
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AFNI Message Board
I want to do the group analysis of functional data. I have the High-Res.Anatomical(SurfVol) and the surface frome freesurfer for each subject. And also I get the experiment's high-Res.Anatomical(ExpVol) along with the functional data.
I do not know if I should do align the surface to experimental data or do map the volumetric data onto surface next.
In my opinion, the SurfVol data has a
by
Linda
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AFNI Message Board
My Afni version is linux_gcc33_64. My system is ubuntu 11.10. So Could you please tell which version will be better for me?
by
Linda
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AFNI Message Board
For the first question, the -GIFTI option is not available for the new @SUMA_Make_Spec_FS. If I use the old version of AFNI to run the @SUMA_Make_Spec_FS. If it can do the will run MapIcosahedron for me. And I am not sure the different between the new @SUMA_Make_Spec_FS and the old version @SUMA_Make_Spec_FS.
by
Linda
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AFNI Message Board
For anatomical data: I get the result from the freesurfer and translate the result by using @SUMA_Make_Spec_FS and then MapIcosahedron.
For functional data: I do the correlation between two condition (different eye watching the same stimulate) within each subject . And then align each subject's the correlation result to the T1.nii (getting from freesurfer) by using 3dAllineate.
1 If I n
by
Linda
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AFNI Message Board