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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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Thank you Paul.
I have another question.
Should I use errts.MCSA1_notlrc.rest.tproject+orig.BRIK or errts.MCSA1_notlrc.rest.anaticor+orig.BRIK for correlation analysis?
by
Naveed
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AFNI Message Board
Hello AFNI experts,
I am using 3dTcorrMap in my analysis to compute the voxel-wise connectivity maps using the following command:
3dTcorrMap -input all_runs.MCSA1_notlrc.rest+orig.BRIK -mask mask_GM_resam+orig.BRIK -Mean Global_1019 -Pmean Global_Pos -Cexpr 'step(r-0.27)*r' TCa027 -CorrMap ind_map -Hist 1000 histo1000
Question 1. How can I set the maximum number of CPU cores fo
by
Naveed
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AFNI Message Board
Hi AFNI experts,
I need to save all the voxel histograms by using the -Hist flag of 3dTcorrMap, however, the maximum limit is 1000, whereas there are 54287 voxels in the mask.
Is there any way to save them all?
by
Naveed
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AFNI Message Board
Hi AFNI experts,
Recently I got the following comments on my manuscript regarding the AFNI preprocessing. Please help to answer these comments:
Following is the detail of the preprocessing steps:
Every single EPI volume was co-registered to the corresponding anatomical image of the subject and mapped to Talairach coordinates space with TT_N27+tlrc template. We exclude first six images
by
Naveed
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AFNI Message Board
Hi,
I have niml.dset cortical thickness files converted from Freesurfer.
I want to see the atlas coordinates in SUMA.
How can I see it? Actually my niml.dset files are the output of 3dMVM, so I do not have the volume files to enable the talk option between SUMA and AFNI.
Thanks in advance.
Naveed
by
Naveed
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AFNI Message Board
Hi,
I have confusion about following two issues
1. For the classification of the fMRI data we can use 3dSVM, is it the only method available in AFNI for classification?
2. As far as I understood I cannot use 3dSVM for niml.dset surface data. Is it correct?
Thanks in advance
Regards
Naveed
by
Naveed
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AFNI Message Board
Dear Gang Chen,
Thank you for the detailed reply.
I have changed the model as you suggested. Please see the following:
3dMVM -prefix ~/MVM_DMN -jobs "12" \
-qVars "age,IQ" \
-bsVars "diag*sex+IQ+age" \
-wsE2 \
-SS_type 3 \
-num_glt 3 \
-gltLabel 1 'TDC-ADHD1-DIAG' -gltCode 1 'diag : 1*tdc -1*adhd1' \
-gltLabel 2 'TDC-ADHDC-DI
by
Naveed
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AFNI Message Board
Dear Gang Chen,
Thank you for your detailed reply.
I want to see the interaction between all the variables both one by one as well as group-wise.
In 3dMVM case should I set -bsVars 'diag+age+IQ" and -wsVars sex ?
Thank you.
Regards,
Naveed
by
Naveed
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AFNI Message Board
Hi,
Following is my code for 3dLME
3dLME -prefix ~/LME_DMN_ADHD200_ALL -jobs 40 -model "diag+sex+age+IQ" -ranEff '~1' -qVars "sex,age,IQ" -SS_type 3 \
-num_glt 24 \
-gltLabel 1 'IQ-DIAG' -gltCode 1 'diag : 1*IQ ' \
-gltLabel 2 'TDC-IQ' -gltCode 2 'IQ : 1*tdc ' \
-gltLabel 3 'TDC-SEX' -gltCode 3 'se
by
Naveed
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AFNI Message Board
Yes, group is the only variable factor. I will run 3dttest++. Thank you.
by
Naveed
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AFNI Message Board
Yes, It is confusing, actually I want to see the combined effect of all 3 groups for functional connectivity maps input. I am not sure 3dLME is what I need for getting this result or I have to perform 3dANOVA2 first?
waiting for your reply,
Thank you
by
Naveed
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AFNI Message Board
HI,
I can not get any output in the 3dLME for the following model, I am unable to understand what is going wrong.
Please help me to correct it
-num_glf 1\
-glfLable 1 'TDC-ADHDC-ADHDI' -glfCode 1 'diag : 1*tdc 1*adhdc 1*adhdi '\
besides this I get all the outputs correctly for glt
waiting for reply
Best Regards
Naveed
by
Naveed
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AFNI Message Board
Hi Rick,
Yes you are right, there are no time files in sMRI data. Isn't it possible to find the connectivity by the correlation technique applied on the single subject using ROI seed, or create a group subject file and then apply the instacorr on it?
by
Naveed
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AFNI Message Board
Hi,
I want to see the correlation between the cortical thickness files.
by
Naveed
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AFNI Message Board
Hi,
Is there any method to apply group instacorr on structural data?
Thanks in advance
Naveed
by
Naveed
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AFNI Message Board
Hi,
Can we apply 3dSVM on the structural MRI data for classification, if yes, is there any sample script available?
Thanks in advance
Naveed
by
Naveed
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AFNI Message Board
Hi rick,
Yes, you are right, I am using the same script for different groups, but how can I fix this error?
I have used the same mask for all the groups, now I can see the results, but im not sure about this fix, is it a correct way?
Thanks,
Naveed
by
Naveed
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AFNI Message Board
Hi Rick,
Following is the complete code that I used.
foreach fred ( *_t1+orig.HEAD )
set sub = `basename $fred _t1+orig.HEAD`
# transform anat to MNI space
@auto_tlrc -base ~/abin/MNI_avg152T1+tlrc.HEAD -input $fred
# transform EPI to MNI as well (assume anat & EPI are aligned)
adwarp -apar ${sub}_t1+tlrc.HEAD -dpar ${sub}_epi+orig.HEAD -resam Cu -dxyz 2.0
# make individual
by
Naveed
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AFNI Message Board
Dear Afni experts,
Please help me to fix the following error
$ 3dGroupInCorr -npb 2 -setA CHR.grpincorr.niml -setB CNT.grpincorr.niml -labelA high_risk -labelB control -center SAME -donocov -seedrad 5
++ 3dGroupInCorr: AFNI version=AFNI_2011_12_21_1014 (Oct 18 2013) [64-bit]
++ Authored by: Cox, the Mad Correlator
++ GIC: data file CHR.grpincorr.data found with 1,960,305,088 bytes of dat
by
Naveed
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AFNI Message Board
Yes u r right, I got better smoothness with 3dmerge
I did the preprocessing by using uber_subject.py
Thanks
Naveed
by
Naveed
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AFNI Message Board
Is this function works similar to this command>>
$ 3dBlurToFWHM -FWHM 10 -automask -prefix conn_smooth -input Connectivity_mask_anat+tlrc
I couldn't find any significant change by running this one.
by
Naveed
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AFNI Message Board
Dear Experts,
I have acquired the seed based connectivity result, but it looks to sparse.
Can anyone suggest me the command to smoothen the AFNI volume file.
I already use the heat kernel on the surface files, but have no idea about the volume smoothing.
Thanks,
Naveed
by
Naveed
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AFNI Message Board
Hi,
Following is the error message, I tried both the command line and GUI versions but same error comes.
Need help
Thanks
$ to3d *.dcm
++ to3d: AFNI version=AFNI_2011_12_21_1014 (Oct 18 2013) [64-bit]
++ Authored by: RW Cox
++ Counting images: total=4060 2D slices
do not recognize image file 1.3.12.2.1107.5.2.32.35413.2010103018272138252028594.dcm
length seen as 120676
** FATAL E
by
Naveed
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AFNI Message Board
YES the output file is in .niml.dset format
and now I can visualize the whole result properly.
In another dataset all the groups have different number of subjects, how can I design an ANOVA experiment with this condition?
Thank you
by
Naveed
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AFNI Message Board
hi,
Some how I have solved all the previous problems :)
new problem is: if I use the bucket output, how can I visualize the contrast files in SUMA viewer?
Thanks
Naveed
by
Naveed
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AFNI Message Board
Hi,
I have solved the above issues now the new error is as follows
$ ./anova_modified.csh
++ 3dANOVA: AFNI version=AFNI_2011_12_21_1014 (Oct 18 2013) [64-bit]
++ Authored by: B. Douglas Ward
Data set dimensions: nx = 49002 ny = 1 nz = 1 nxyz = 49002
** FATAL ERROR: Program 3dANOVA2: sample size is too small for fixed effects model
** Program compile date = Oct 18 2013
$
Is i
by
Naveed
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AFNI Message Board
Hi Gang,
I have modified my code as follows but stilli receive error on execution
# For the 2-way Anova
# alevels = Diagnosis groups 1 = CNT, 2 = CHR, 3 = FEP
# blevel = No of subjects per group = 28 each
set dir_chr = /media/sf_D_DRIVE/Freesurfer_Data/Processed/CHR
set dir_cnt = /media/sf_D_DRIVE/Freesurfer_Data/Processed/CNT
set dir_fep = /media/sf_D_DRIVE/Freesurfer_Data/Processed/
by
Naveed
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AFNI Message Board
hi,
Factor A is gender, and factor B is the category of subjects, number of subjects are 24, 36 and 28 respectively in three groups.
Thanks
by
Naveed
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AFNI Message Board
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Pages: 123