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
Page 2 of 4
Pages: 1234
Results 31 - 60 of 94
Hi,
This is my script:
=============
#!/bin/bash
#this function used for extracting the beta value of each interaction iterm each subject
cd /home/zhangxiaochu/zharj/igt_ddt/ddt
curr_path=`pwd`
output_path=$curr_path/interaction_regress
data_dir=$curr_path/function115
psycho1=all_hard
psycho2=all_easy
var_num=18
#var_num=15
var_num=13
var_name=allrun
cd $data_dir
sbname=`ls`;
by
charujing123
-
AFNI Message Board
Hi Gang
Ok, I see.
Looking forward some update in the machine learning, as 3dsvm is not enough.
Thanks,
Best.
Rujing
by
charujing123
-
AFNI Message Board
Hi Gang
I see. However, in , Page 9, it shows
======
4) Network-level test:
multivariate model (MVM)
{FA1 , FA2, FA3, ...}~ var1 + var2 + var3 ...
======
Here is my idea about this test: multi-X was used to test the effect on the multi-Y. And the ys are brain connectivity acquired from the DTI data. It should be similar to voxel by voxel activity.
If this idea was correct, then i can us
by
charujing123
-
AFNI Message Board
hi paul, i think the netpbm is already in my macos.
=====
bash-3.2$ brew install netpbm
Warning: netpbm 10.73.22 is already installed and up-to-date
To reinstall 10.73.22, run `brew reinstall netpbm`
=====
Here is the output in the command during running the
===============
"# I/O path, same as above; just need the "proc" dirs now
set path_P_ss = /Users/caroline/CON_IA27/
by
charujing123
-
AFNI Message Board
Hi
After running the program, there was no PNG in the anat_01.
Here is the program I used.
# I/O path, same as above; just need the "proc" dirs now
set path_P_ss = /Users/caroline/CON_IA27/fatcat/data_proc/SUBJ_001
# reference anatomical volumes to which we axialize
set here = $PWD/fatcat_proc_mni_ref
set ref_t2w = $here/mni_icbm152_t1_tal_nlin_sym_09a_MSKD_ACPCE.nii.
by
charujing123
-
AFNI Message Board
Dear afni experts,
Can 3dmvm perform the cross-validated MANOVA as described in this paper ?
Thanks,
Best
Rujing
by
charujing123
-
AFNI Message Board
Hi Paul
Thanks for your reply. I am a learner in Guangzhou, China, and asked you how to correct multiple comparisons during that program. And you said only ROI-based bayesian from Gang Chen can be used to perform the correction. Do you remember?
After the trainning program, I searched on the AFNI command and found that SurfClust could "Usage: A program to perform clustering analysis surfac
by
charujing123
-
AFNI Message Board
hi all
i am very happy to find SurfClust which can perform the multiple correction on surface based analysis. It is difficult for me to write the code for this, although I read the help of the SurfClust. OK. Here are output for my script:
========
- Error SUMA_SurfClust_ParseInput (SUMA_SurfClust.c:437):
Option -i not understood.
Try -help for usage
Here's hoping these excerpts
by
charujing123
-
AFNI Message Board
I have used this script below. Does this mean that the datasets were non-linearly transformed to MNI space?
afni_proc.py -subj_id $sb \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat ${sb}_SurfVol.nii \
-anat_follower_ROI aaseg anat aparc.a2009s+aseg.ni
by
charujing123
-
AFNI Message Board
Hi
-RHS rset = Specifies the right-hand-side 3D+time dataset.
('rset' can also be a 1D file with 1 column)
* Exactly one '-RHS' option must be given to 3dTfitter.
I wonder what is right-hand-side fMRI data? In general, we aquired one 3D+t fmri data in the MR.
by
charujing123
-
AFNI Message Board
In ,
And in the end you may need to down-sample the interaction time series back to TR grids by running
1dcat Inter_A.1D'{0..$(xx)}' > Inter_Ad.1D
However, this code cannot downsample, but extract numbers from 0 to xx.
by
charujing123
-
AFNI Message Board
Hi
Thanks for your reply. I want to perform PPI analysis. After this afni_proc.py, regression analyses with PPI regressor will be performed in the following script with 3dDeconvolve. This is because I do not know how to set PPI regressor in the afni_proc.py.
by
charujing123
-
AFNI Message Board
afni_proc.py -subj_id $sb \
-blocks tshift align tlrc volreg blur mask scale \
-copy_anat ${sb}_SurfVol.nii \
-dsets \
${path_dest}/function/$sb/func1/func1+orig.HEAD \
${path_dest}/function/$sb/func2/func2+orig.HEAD \
by
charujing123
-
AFNI Message Board
Hi
I wonder differences between the despike (in -blocks) and outlier (-regress_censor_outliers).
thanks.
by
charujing123
-
AFNI Message Board
Hi
Thanks for your kind help. Running the fmri data using afni_proc.py is time intensive. Furthermore, I have too many subjects. I want to do follow steps, but I donot know which afni code can help me:
1, using FWHM=8mm, and generating results.
2,using results of 1 as master, then apply fwhm=4mm results to this master.
thanks.
by
charujing123
-
AFNI Message Board
Hi
I have run my resting data using afni_proc.py. However, I see the blur size was 4mm. So how to apply 8mm to the errts*+tlrc data without running the afni_proc.py again?
by
charujing123
-
AFNI Message Board
Hi
So which value I used for the Euclidean norm would be appropriate?
Thanks
Rujing
by
charujing123
-
AFNI Message Board
Hi all
Does the -regress_censor_motion in afni_proc.py meant Framewise displacement (FD)?
If so, it is calculated by the absolute value of derivatives of the six realignment parameters or RMS of those?
Thanks.
Rujing
by
charujing123
-
AFNI Message Board
Hi all
I am interested in the differences between Total Intracranial Volume and brain size. Someone can tell me that?
Thanks.
Best
Rujing
by
charujing123
-
AFNI Message Board
Hi ,
I have downloaded "Download AFNI/SUMA Software for Linux ( xorg7 64bit ) ". However it echo this
=============
$ 3dAllineate
3dAllineate: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
$ file 3dAllineate
3dAllineate: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs),
by
charujing123
-
AFNI Message Board
$ make @SUMA_Make_Spec_FS
make: *** No rule to make target `@SUMA_Make_Spec_FS'. Stop.
That is why?
Thanks.
by
charujing123
-
AFNI Message Board
Hi
Thanks. I see. the final file "err*fanaticor+tlrc*" has 1198TRs, however, the terminal said conflict results (see attached file). So why the err*fanaticor+tlrc* was not censored?
Thanks.
by
charujing123
-
AFNI Message Board
Hi
I have split my resting data into two parts, then the program worked. The two preprocessed data will be 3dTcat for the functional connectivity analysis. Is that OK?
Thanks.
by
charujing123
-
AFNI Message Board
Hi
thanks. I also met same problem, and resolve it using your suggestions.
Best.
by
charujing123
-
AFNI Message Board
I have tried it for several times.
One time one subject.
It is always terminated in that step..
by
charujing123
-
AFNI Message Board
Page 2 of 4
Pages: 1234