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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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Hi rick,
The output of this command is like this:
"tianshu@ubuntu:~/Desktop/1/dicom$ 3dinfo mean+orig.
++ 3dinfo: AFNI version=AFNI_22.1.13 (Jun 6 2022) [64-bit]
Dataset File: mean+orig
Identifier Code: AFN_egxtYprYQt_yRXf_CDX5Bg Creation Date: Tue Jun 21 01:05:18 2022
Template Space: ORIG
Dataset Type: Func-Bucket (-fbuc)
Byte Order:
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Sue_TS
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AFNI Message Board
Hi experts,
I was using 3dSkullStrip to remove skull of mice images by following command:
"3dSkullStrip -prefix mask -orig_vol -input base+orig"
where "base+orig" came from "3dTstat -prefix base -mean function.nii".
And I got error message like this:
"-- Error SUMA_LoadPrepInVol (SUMA_BrainWrap.c:77):
98 percentile is 0!
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Sue_TS
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AFNI Message Board
Hi,
We are using 3dTcorrMap to calculate a whole brain correlation map, here is our command line:
3dTcorrMap -input pb05.S007.scale+orig. -mask mask_anat.S007+orig. -polort -1 -Mean S007_Tmap -Zmean S007_Zmap
BUT the value of all the voxels in our output dataset is 1, like the picture I uploaded.
Does anyone know what's wrong with my analysis?
All the best
Tianshu
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Sue_TS
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AFNI Message Board
Hi pt,
Indeed, I did some ROI-based correlation analysis by 3dNetcorr, it calculated the mean value of the ROIs then get the correlation among them.
What I want is voxel-voxel correlation like the function of 3dTcorrMap.
To get a functional ‘connectedness’ maps by calculating the correlation (Pearson’s r) of the residual time series in each voxel of Amygdala with every other voxel in another
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Sue_TS
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AFNI Message Board
Hi,
I am doing some analysis about voxel-voxel correlation on my resting-state fMRI data by 3dTcorrMap, the program is doing well on whole brain analysis(using whole brain mask).
I wander that is that possible to calculate the voxel-voxel correlation between one ROI and another different ROI(like Amygdala and Hippocampus)?
I did not find proper option in the help-file :( .
Expecting to he
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Sue_TS
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AFNI Message Board
It seems to be the problem of the memory space because my %CPU is over 90% when running 3dTcorrMap :(.
It's really impossible for me to update my computer recently, so I guess I could import my data into the MATLAB to finish this analysis, but my code couldn't work.
Here's my core command in AFNI.MATLAB:
"=size(Vmask);
TcorrMap=zeros(x_size,y_size,z_size);
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Sue_TS
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AFNI Message Board
Hi Rick,
To save the space, I have applied the GMe mask on my data and all of my grids were resampled to 2 mm^3.
According to the given information, it seems like that it has began to compute my data but somehow crashed suddenly, I really have no idea about that.
Best regards,
Sue
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Sue_TS
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AFNI Message Board
Hi all,
I got a problem when I was running 3dTcorrMap for my Whole-Brain Voxel-Voxel
Correlation analysis, the program always kill itself without any reason like this:
3dTcorrMap -input y03.r01.bp+tlrc. -mask y03.r01.bp+tlrc. -polort -1 -CorrMap wb_map -CorrMask
++ 3dTcorrMap: AFNI version=AFNI_17.1.10 (Jun 6 2017) [64-bit]
++ Number of voxels in mask = 103704
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Sue_TS
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AFNI Message Board
In my case, I finally found that my 2 ROIs were named the same in the beginning... :(
It's such a stupid problem but took me a few days to discover, an unforgettable experience.
Sorry for replying too late, hope you have solved your problem.
Sue
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Sue_TS
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AFNI Message Board
I have solved the problem, thank you anyway!!!
Best regards,
Sue
by
Sue_TS
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AFNI Message Board
Hi,
Sorry I didn't describe my problem clearly and didn't give the actual results. Here is my output:
y:/media/y/1E9042E09042BDD1/Resting/y02/y02.results> 1dCorrelate r$run.dy1.PCC.1D r$run.dy1.LmFC.1D
# Pearson correlation
# Name Name Value BiasCorr 2.50% 97.50% N: 2.50% N:97.50%
# ------------------ ------------
by
Sue_TS
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AFNI Message Board
Hi all,
I am trying to do some dynamic analysis on my resting data, I extract the mean value of my ROIs in different time window and then calculate their Correlation with 1dCorrelate like this:
3dmaskave -mask $subj.r$run.PCC+tlrc. -q errts.$subj.r$run.e2t+tlrc.'[0-49]' > r$run.dy1.PCC.1D
3dmaskave -mask $subj.r$run.LmPFC+tlrc. -q errts.$subj.r$run.e2t+tlrc.'
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Sue_TS
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AFNI Message Board
Hi AFNI friends,
Thank you sooooo much for your help!!!:)
My problem has been solved now, I couldn't run the script @snapshot_volreg and @chauffeur_afni because of the missing of xvfb package rather than netpbm package.
Thank you again.
Best regards,
Sue
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Sue_TS
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AFNI Message Board
Hi Bob,
Thanks a lot for your advice and it seems to be a suitable method for me.
But it requires the netpbm11 software, which is difficult to install on my ubuntu 16.04 system:(, I'll keep trying.
I wonder if the script @AddEdge can also reach my goal?
Best regards,
Sue
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Sue_TS
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AFNI Message Board
Hi all,
I,m trying to align my anatomical data to the TT_N27+tlrc template,
but the gyrus and sulcus are not aligned very well so I tried different ways such as auto_warp.py and @auto_tlrc,
I wonder if there is a commend or something else in AFNI could help me to evaluate the results of Talairach alignment?
Best regards,
Sue
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Sue_TS
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AFNI Message Board
Hi, Pt
GSL isn't installed on my computer.
Here is the result of afni system check:
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.8.0-58-generic
version: #63~16.04.1-Ubuntu SMP Mon Jun 26 18:08:51 UTC 2017
distribution:
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Sue_TS
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AFNI Message Board
Hi pt,
1>, Could you please copy/paste the full output of the message returned in the terminal?
The command line and full output:(Sorry I don't know how to uploading the txt file )
y:/media/y/1E9042E09042BDD1/Resting/y02/y02.results> 3dNetCorr -inset pb05.y02.r01.e2t+tlrc. -in_rois BNST+tlrc Amy+tlrc. -fish_z -ts_wb_corr -prefix restcorr_Amy
++ Reading in.
++ Allocating...
+
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Sue_TS
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AFNI Message Board
Hi all,
I am trying to analyse some rs-fMRI data with AFNI and I have a question about 3dNetcorr.
I want to get the ROI-ROI function connectivity so I tried to run the following commands:
3dNetCorr \
-inset pb05.{subj}+tlrc. \
-in_rois FFA+tlrc OFA+tlrc \
-fish_z
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Sue_TS
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AFNI Message Board
Hi
I have a question about 3dTcorrMap
I tried to run the following commands:
3dTcorrMap -input brain+tlrc -CorrMap test1
3dTcorrMap -input brain+tlrc -seed brain+tlrc -CorrMap test2
I think I should get the same output for test1 and test2. However, the values in test2 were much smaller than test1. can anyone tell me what I miss here?
More for option -CorrMask, I cannot get the sub bri
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Sue_TS
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AFNI Message Board