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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
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Thank you very much for your help.
I could successfully convert my data.
Respectfully,
Sanaz
by
Sanaz_khosravani
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AFNI Message Board
Dear AFNI Members,
I needed to convert my anatomical data generated in the MNI space (by the SPM software) to TT space. I encountered the command auto_tlrc, but if I understood correctly, if the original anatomical file is in MNI space, this command will not standardize our data to TT space.
Thank you very much in advance.
Respectfully,
Sanaz
by
Sanaz_khosravani
-
AFNI Message Board
Also, my second question was that because gender is a categorical variable, in my previous attempts with 3dMVM I used to use letters (F/M) in the covariates file. But in the 3dttest++ we are instructed to only use numeric variables as a covariate. Accordingly, I have used 1 for females and 0 for males. I was just concerned that the algorithm may treat the data differently if a categorical covaria
by
Sanaz_khosravani
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AFNI Message Board
Dear All,
I am using the 3dttest++ for comparing two different groups of subjects and would like to control for the effect of gender as a covariate. I referred to the help file of the 3dttest and found the following illustration on the structure of the output:
-------------------------------
STRUCTURE OF THE OUTPUT DATASET ~1~
-------------------------------
* The output dataset is s
by
Sanaz_khosravani
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AFNI Message Board
I very appreciate it, Dr. Gang.
When I code with + or * the error does not change:
3dMVM -prefix COMPARE_masked_all3 -jobs 1 \
-bsVars 'group+class' \
-SS_type 3 \
-num_glt 3 \
-gltLabel 1 G1_vs_G2 -gltCode 1 'group : 1*G1 -1*G2' \
-gltLabel 2 G3_vs_G2 -gltCode 2 'group : 1*G3 -1*G2' \
-gltLabel 3 G1_vs_G3 -gltCode 3 'group : 1*G1 -1*G3' \
-mask
by
Sanaz_khosravani
-
AFNI Message Board
I very appreciate it, Dr. Gang.
Please find the following lines containing the content of the Terminal messages:
3dMVM -COMPARE_masked -jobs 1 \
> -bsVars 'group*class' \
> -SS_type 3 \
> -num_glt 1 \
> -gltLabel 1 FSD_vs_HV -gltCode 1 'group : 1*FSD -1*HV' \
> -mask mask_resamp_bin+tlrc. \
> -dataTable @dataTable_new.txt
Read 300 items
Loading
by
Sanaz_khosravani
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AFNI Message Board
Dr. Chen,
I appreciate your time indeed.
Unfortunately, removing the line qVars did not help with the problem. I tried adding or removing some options but am still receiving an error. Here is the code I used:
3dMVM -prefix COMPARE -jobs 1 \
-bsVars 'group*relation' \
-SS_type 3 \
-num_glt 1 \
-gltLabel 1 G1_vs_G2 -gltCode 1 'group : 1*G1 -1*G2' \
-dataTable @dataTa
by
Sanaz_khosravani
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AFNI Message Board
Dr. Chen,
I appreciate your help very much. Correction of the dataTable file solved the issue.
I ran the code excluding the covariate as follows and got the output file that I could plot as well. Here is the code that worked fine:
3dMVM -prefix G1_G2_G3_COMPARE -jobs 1 \
-bsVars 'group' \
-SS_type 3 \
-num_glt 1 \
-gltLabel 1 G1_vs_G2 -gltCo
by
Sanaz_khosravani
-
AFNI Message Board
Thank you very much for your time and for helping me with running this algorithm.
I focused on 3dMVM only and generated the following lines of code:
3dMVM -prefix G1_G2_COMPARE -jobs 1 \
-bsVars "group*gender" \
-num_glf 1 \
-glfLabel 1 G1_vs_G2 -glfCode 1 'group : 1*G1 -1*G2' \
-dataTable @G1_G2_dataTable_new.txt
with the dataTable file being:
Subj gr
by
Sanaz_khosravani
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AFNI Message Board
I appreciate your response.
In this study we have one between-subject variable and one between-subject covariate. The example I posted here, was a test run in which only two groups were considered, but the actual research examines three groups. If I have understood the methods correctly, the 3dttest method is only valid for two groups, and the 3dANOVA command is valid when there are no covari
by
Sanaz_khosravani
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AFNI Message Board
Dear All,
I was trying to run 3dMEMA to compare two different groups, using the following lines of code, but when I plot the output in the AFNI GUI no activation is observed:
3dMEMA -prefix G1_G2_COMPARE \
-jobs 1 \
-groups G1 G2 \
-set G1 \
s305 stats.s305+tlrc'[7]' stats.s305+tlrc'[8]' \
s307 stats.s307+tlrc'[7]' stats.s307+tlrc'[8]'
by
Sanaz_khosravani
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AFNI Message Board
I just wanted to update that I changed from bash to tcsh and it worked fine.
by
Sanaz_khosravani
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AFNI Message Board
Dear All,
Thank you for your consideration to my inquiry.
I was trying to run group comparisons using ANOVA based on the following lines of code:
3dANOVA -levels 3 \
> -dset 1 address for the variable \
.
.
.
> -dset 2 address for the variable \
.
.
.
> -dset 3 address for the variable \
.
.
.
> -mean 1 group1\
> -mean 2 group2\
> -mean 3 gro
by
Sanaz_khosravani
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AFNI Message Board
Dr. Reynolds,
Thank you very much for your response and guidance.
Respectfully,
Sanaz
by
Sanaz_khosravani
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AFNI Message Board
Dear All,
We are working on a dataset in which our task is triggered by a series of auditory stimuli. We switched to a different fMRI scanner at some point in the study and with regard to the data collected on the new scanner, we are observing no brain activation for the study participants. We have checked if the stimulus files are being generated correctly, and if the initial TRs are being re
by
Sanaz_khosravani
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AFNI Message Board