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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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In other probabilistic tractography method, it was applied by sampling 5000 streamline fibers per voxel. For a seed region, 5000 × n fibers were sampled; n is the number of voxels in the region. The number of fibers passing through a given region divided by 5000 × n is calculated as the connectivity probability from the seed region to the given region.
In the 3dTrackID, it used several options
by
chaj
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AFNI Message Board
Hi Paul,
AFNI lectures were very helpful for me to understand the concept of DTI.
But I have still some questions which I couldn’t solve from lecture notes.
My main question is for FA connectivity matrix and NT connectivity matrix.
1. Whole brain FA map can be obtained before tracking process. In order to calculate FA connectivity matrix (ROIs by ROIs), I ran 3dTrackID for probabilistic tr
by
chaj
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AFNI Message Board
Hi,
I am doing DTI analysis by FATCAT and TORTOISE pipeline.
After running 3dTrackID for the Probabilistic tracking, I could get several matrices. FA-based connectivity matrices, Number of streamlines, etc.
I want to ask how these connectivity matrices were calculated between ROIs and also what is the meaning of these matrices.
Thanks,
Jung
by
chaj
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AFNI Message Board
Hello,
I am trying to calculate the resting state functional connectivity(RSFC) map.
3dNetCorr does not support to use eigen value of ROI time series, so I would like to use 3dfim+ which will use 1D time series file that I input (eigen value timeseries of the ROI) and calculate the RSFC map to the whole brain.
But, 3dfim+ description is saying that "This program (3dfim+) is very old,
by
chaj
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AFNI Message Board
Hi,
I have question about running 3dTrackID. I have used this command for several data, but some data gave me the error message. I followed AFNI FATCAT pipeline for DTI processing.
Here is my command
3dTrackID \
-mode PROB \
-dti_in dt \
-netrois sel_indt_aparc.a2009s+aseg_REN_gm_GMI.nii.gz
by
chaj
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AFNI Message Board
Thank you.
3dPVmap seems working only for calculating principal components. If I have got eigen time series from it, is there any way to generate functional connectivity matrix using calculated eigen time series?
When I take a look at the function of 3dNetcorr, it does not have any option to use input that calculate externally but only it might start from calculating mean time series and us
by
chaj
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AFNI Message Board
Hi,
I would like to ask about the resting state functional connectivity matrix(RS-FC matrix).
By 3dNetCorr, I could make RS-FC matrix derived from mean time series. I want to make RS-FC matrix using eigen time series.
Is there any way to extract eigen time series and make RS-FC matrix in AFNI?
Thanks
Jung
by
chaj
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AFNI Message Board
Hi Paul,
Thanks for your response.
In my TEST01_scri.tcsh,
3dMVM -prefix TEST01_MVM \
-bsVars "Group+Scanner+Age+Sex+Race+HAMD+YMRS" \
-wsVars "ROI" \
-qVars "Age,HAMD,YMRS" \
-dataTable @TEST01_MVMtbl.txt
I have removed 'glt' parts to reduce computation cost, but still same empty result has shown.
As your suggestion, I tried t
by
chaj
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AFNI Message Board
Hi,
I am running FAT_MVM to see main effect of group with Functional connectivity(FC) matrix.
Each subject has a 195*195 size FC matrix, and I try to do group analysis with 180 subject.
I have followed FAT_MVM demo and apply this same way to my analysis.
1) To get data table, I ran
fat_mvm_prep.py -p TEST01 -c all_subj_Cross_Bandpass_3Group.csv \
-m 'Cro
by
chaj
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AFNI Message Board
I have some questions about group-level DTI analysis. I have .grid files from each subjects. I want to run group-level analysis with them.
1-1) I am going to use FATCAT_MVM for this. I need to run fat_mvm commands with .grid files and . csv files.
My experiment is looking at the longitudinal study with medication effect, for example, subj01 in group A has been scanned four times at week 1,
by
chaj
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AFNI Message Board
Thanks.
In this case, if I use contrast image, for example ' pos_neu = pos -neu' and ' nag_neu= neg- neu'
and apply them to 3dLME,
a) -gltLabel 1 'pos-neu' -gltCode 1 'cond : 1*pos -1*neu' \
b) -gltLabel 8 'pos-neg_contrast' -gltCode 8 'cond : 1*pos_neu -1*neg_neu' \
I expected the similar result, but it also gave totally di
by
chaj
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AFNI Message Board
Hi,
I would like to ask about 3dLME GLT coding.
I just bring the 'example 3' from '3dLME' instruction on the web as following.
3dLME -prefix Example3 -jobs 24 \
-model "cond*group" \
-ranEff '~1' \
by
chaj
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AFNI Message Board
I am trying to save images automatically by using this command :
afni -noplugins -no_detach \
-com 'SET_XHAIRS A.OFF' \
-com 'OPEN_WINDOW A.axialimage mont=9x9:1'\
-com 'OPEN_WINDOW A.coronalimage mont=9x9:1' \
-com 'OPEN_WINDOW A.sagittalimage mont=9x9:1' \
-com 'SWITCH_UNDERLAY A.img.nii' \
-com 'SAVE_JPEG A.sagittalimage ./c
by
chaj
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AFNI Message Board
I have a question about volume rendering.
Now I am using the atlas 'CA_ML_18_MNIA' which has 116 ROIs. I would like to perform 3D visualization of each ROIs from this atlas.
I have tried AFNI Renderer on AFNI GUI, but it seems be hard to control images.
If I want to use SUMA for this, what should I do first? for example how to make the input for SUMA.
Thanks
Jung
by
chaj
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AFNI Message Board
Hi,
I am using 'CA_ML_18_MNIA' atlas for my analysis.
I could find 'MNIa_caez_ml_18+tlrc.' file from the afni and ran '3dinfo' to check how many ROI this atlas has.
Dataset File: MNIa_caez_ml_18+tlrc
Identifier Code: AFN_BtpG7XnhUGbf2-vZfx6umQ Creation Date: Tue Jun 14 13:57:42 2011
Template Space: MNI_ANAT
Dataset Type: Spoiled GRASS (-spgr)
Byte
by
chaj
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AFNI Message Board
Does Afni folder have 'MNI_caez_ml_18+tlrc'?
In my AFNI folder, there is only 'MNIa_caez_ml_18+tlrc', I can't find 'MNI_caez_ml_18+tlrc'.
by
chaj
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AFNI Message Board
As my understanding, MNIa is the shifted version of MNI.
When I see my statistical results on the AFNI GUI, and I checked the location of peak voxel by using 'whereami' function.
From this, ROI name is given according to MNIa atlas not MNI atlas.
1) Why do we need MNIa instead of MNI atlas in the 'whereami' on the AFNI GUI?
2) If I use 'MNI_caez_ml_18+tlrc'
by
chaj
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AFNI Message Board
I need to transform the following two atlas to MNI space(I am using 2.5mm^3 resolution MNI mask which I resampled for my data) .
CA_ML_18_MNIA MNI_ANAT /home/afniHQ/afni.build/pub.dist/bin/linux_ubuntu_16_64//MNIa_caez_ml_18+tlrc Macro Labels (N27)
TT_Daemon TLRC /home/afniHQ/afni.build/pub.dist/bin/linux_
by
chaj
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AFNI Message Board
For 2),
Can I ask you what kind of registration is used?
For example, if I have a template on Talairach space (Each ROI would has an integer value for labeling) and try to transform this template to MNI space, I assume that this MNI-registered template would not have integer value(maybe it would be floating number) to represent ROIs since we performed registration.
I need MNI-registered te
by
chaj
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AFNI Message Board
Hi,
I have some questions about using 3dmaskave or 3dROIstats
1) If I want to compute the average time series of epi_r1+orig over ROI1+orgi, I can use
3dmaskave -mask ROI1+orig epi_r1+orig
But If I would like to do same thing over whole ROI from the atlas (for example, MNIa_caez_ml_18+tlrc, or TTatlas+tlrc),
do I need to do it in the 'for loop' from ROI1 to ROIlast? o
by
chaj
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AFNI Message Board
Hi,
I have some questions about 3dsvm.
I am trying to run 3dsvm for classifying multi-class groups(in my case, four groups) from task-related fMRI data.
GroupA : 30 subjects
GroupB : 40 subjects
GroupC : 28 subjects
GroupD : 32 subjects
1) To generate 'TrainVol'(4D volume=3D beta images from each subject * # of subjects), should all 'TrainVol' from each group h
by
chaj
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AFNI Message Board
I use '1dDW_Grad_o_Mat++' for DTI analysis.
''1dDW_Grad_o_Mat++' just converts the type of bvec, or the sign(+/-) of some values from bvec can be changed?
Jung
by
chaj
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AFNI Message Board
Are these post hoc tests produced by 3dLME by itself or do we have to specify this?
For example I have group1 (condition1 condition2) group2 ( (condition1 condition2) group3 (condition1 condition2) so to look at the group difference between group1 and group2 for condition difference condition1 and condition2, I would have to do this
-gltLabel 1 group1_2 -gltcode 1 'group: 1*group1 -1*
by
chaj
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AFNI Message Board
In the TOP_DIR, I have two directories (DTI-1 and DTI-2), each directories has DWI dicom files.
I ran fat_proc_convert_dcm_dwis -indir "./TOP_DIR/DTI-1" -prefix ./TOP_DIR/DTI-1/DWI/dwi1 and
fat_proc_convert_dcm_dwis -indir "./TOP_DIR/DTI-2" -prefix ./TOP_DIR/DTI-1/DWI/dwi2
I obtained
in the ./TOP_DIR/DTI-1/DWI/, dwi1.nii.gz, dwi1_bval.dat, dwi1_cmd.txt
by
chaj
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AFNI Message Board
I have a question about DTI analysis acquired on the 3T.
In this I have 2 sessions of DTI ( DTI-1, DTI-2) for each subject.
I am using AFNI FATCAT TORTOISE pipeline. To get DTI volume and b-vec files from dicom files, '‘fat_proc_convert_dcm_dwis’ is performed with DTI-1 and DTI-2 separately. Output will be 2 sets of DTI data, each of which have dwi.nii.gz, dwi_bval.dat, dwi_cmd.txt, d
by
chaj
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AFNI Message Board
In our study we have 4(levels) groups and 2(levels) conditions so we looked at the main effect of group x condition.
Now we want to look at the post-hoc that is the group differences between any 2 groups, to do that we have extracted the beta values form the regions of group x conditionresults and performed ANOVA in SPSS.
Would this be a right way of showing the post-hocs or should we just do
by
chaj
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AFNI Message Board
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