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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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Pages: 12
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Turns out I spoke too soon. While the command
afni_proc.py -subj_id NI01_SMc -dsets run1+orig run2+orig run3+orig run4+orig -blocks tshift volreg blur mask scale regress -copy_anat anat+orig -do_block align tlrc -volreg_align_to last -volreg_align_e2a -volreg_tlrc_warp -blur_in_automask -regress_stim_times stimes.NT1.1D stimes.NT2.1D stimes.NT3.1D stimes.ND1.1D stimes.ND2.1D stimes.ND3.1D stim
by
Sabrina
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AFNI Message Board
Hi Rick,
I found my error that caused the mistake in the earlier post and have corrected it. It runs now. My supervisor was wondering if there is any way of utilizing a more up-to-date processing, the 3dDeconvolve on the binary txt file. Would that be possible?
by
Sabrina
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AFNI Message Board
I followed your advice and ran
waver -input Sample_a.txt -GAM -dt 2 > SAM.1D
waver -input nTAR1_a.txt -GAM -dt 2 > NT1.1D
waver -input nTAR2_a.txt -GAM -dt 2 > NT2.1D
waver -input nTAR3_a.txt -GAM -dt 2 > NT3.1D
waver -input sTAR1_a.txt -GAM -dt 2 > ST1.11D
waver -input sTAR2_a.txt -GAM -dt 2 > ST2.1D
waver -input sTAR3_a.txt -GAM -dt 2 > ST3.1D
waver -input nDIS1_
by
Sabrina
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AFNI Message Board
I fixed the mistakes you mentioned. THe masks still look very small in particular in the forebrain region. Is there any way of enlargening them, like a BLUR command?
Thank you
Sabrina
by
Sabrina
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AFNI Message Board
Rick,
I am completely at a loss with them. I have *.txt files that consist of nothing but a single column of 0 and 1. I have an example of a .1D file that contains a single column with this which repeats several times between the 0.507025 and all the 0s. I honestly have no idea how to make them into meaningful stim files that I can use and am having a very hard time following the descriptions
by
Sabrina
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AFNI Message Board
Thank you!!
BTW, is there any way to blur a mask made by using the TT Daemon? Some of the masks that I made with it are very small and cutting off areas that are still part of the ROIs of the brain. I used the following commands (samples down below).
3dcalc -a TT_Daemon::Brodmann_area_4 -expr 'step(a)' -prefix ba4
3dcalc -a ba4+tlrc. -expr 'step(a*x)' -dicom -prefix ba4
by
Sabrina
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AFNI Message Board
Hi,
I am wondering if this is correct, trying to check my data processing with my predecessors from 3 years ago who no longer work here. I am trying to make stim files and can't find any information since afni webpages except for the message board appear to be down again, the second time this month. Could you please tell me if this procedure correct for making stim files?
Thank you very
by
Sabrina
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AFNI Message Board
Thank you.
How do I get afni to give me volume (ml or mm3) measurements from the mask? What command do I have to use?
by
Sabrina
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AFNI Message Board
I tried uploading my pictures from the UNIX computer I am using but am unable to do so to this website. Apparently the *.jpeg format is not compatible and it refuses to upload my pictures.
I have 2 different datasets that are causing me trouble. The first where the functional overlay is still too "high" from the anatomical dataset, resulting in cortical masks being above the cortica
by
Sabrina
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AFNI Message Board
I am trying to draw my own ROIs and would like to measure the volume contained within them. I was trying to get afni to extrapolate ROIs in intermediate sections if I only use every third section to hand draw the ROI and am having a hard time understanding the documentation I found.
I am trying to measure the volume of the lateral, third and fourth ventricle as well as the whole brain volume for
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Sabrina
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AFNI Message Board
Can afni be used to make volume measurements of the whole brain, brain regions and ventricles using the anat.file with skull?
by
Sabrina
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AFNI Message Board
I added the additional command lines. Does it matter where I insert them? Also, the EPI still is high, is there any other way to adjust the EPI? Can it be manually moved to match the anatomy?
by
Sabrina
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AFNI Message Board
Thank you, although the EPI is still a bit high, it did improve the overlay when viewing in afni. I will see how the data looks.
I have a different question concerning another overlay. There is a ghost in the anatomical data as seen in the attached jpg file. The overlay in the screen shot shows the overlay using the TSNR file over the anat_final file. The ghost is not covered. Does that mean
by
Sabrina
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AFNI Message Board
I used the following commands before using masks based on the TT_Daemon standard.
Thank you!
$ to3d -time:zt 36 163 2000 alt+z2 *.IMA
$ afni_proc.py -subj_id NI12_SMc -dsets run1+orig run2+orig run3+orig run4+orig -blocks tshift volreg blur mask scale regress -copy_anat anat+orig -do_block align tlrc -volreg_align_to last -volreg_align_e2a -volreg_tlrc_warp -blur_in_automask -regress_stim_t
by
Sabrina
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AFNI Message Board
Hi,
After pre-processing and using
$ tcsh -xef proc.NI17 |& tee output.proc.NI17
I have a non-matching overlay as shown in the attached file. The procedure worked for all other files. How can I move the overlay "down" to fit the scan?
Thank you very much!
Sabrina
by
Sabrina
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AFNI Message Board
The multimask is based on the TT_Daemon using Brodmann areas. I tried to not have them touch, yet, this multimask if giving trouble:
3dcalc -a ba19_left+tlrc -b acc_left+tlrc -c parah_left+tlrc -expr 'step(a)+2*step(b)+3*step(c)' -prefix LeftMultiRegion_mask3
After fractionization I receive the notice:
Found 4 distinct nonzero values
And when I use it to measure my data I get 4
by
Sabrina
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AFNI Message Board
I did that and received a BRIK and HEAD file. I don't understand what the information in them tells me. In afni, the brain is mostly red.
I do know I am looking at several adjacent Brodmann areas, so chances are that the ROIs may overlap. To eliminate that, I guess I will make several multimasks with non-touching Bradmann areas. Is there any way to have the means in the resulting txt fil
by
Sabrina
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AFNI Message Board
I made a multimask specific for each hemisphere and then measured my data with it. The results show no labels which mean corresponds to which ROI (am guessing they are in order described in multimask) and I have 6 addiotional columns that I don't know what they are. Any idea how I can identify the data within them? I used the following commands to make my multimask:
3dcalc -a ba4_left+tl
by
Sabrina
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AFNI Message Board
Thank you for your help, Daniel.
I have a question to the results I am getting after used my multimask based on the folowing commands:
$ 3dcalc -a ba4_right+tlrc -b ba6_right+tlrc -c ba7_right+tlrc -d ba8_right+tlrc -e ba9_right+tlrc -f ba10_right+tlrc -g ba17_right+tlrc -h ba18_right+tlrc -i ba19_right+tlrc -j ba24_right+tlrc -k ba32_right+tlrc -l ba37_right+tlrc -m ba40_right+tlrc -n ba45_
by
Sabrina
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AFNI Message Board
Does this mean that I can't make a multimask like before but have to make an individual one for each side of each Brodmann area of interest?
by
Sabrina
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AFNI Message Board
When I use the following command for making a multimask, can I identify left and right in the results?
Thank you very much!!!
3dcalc -a TT_Daemon::Brodmann_area_17 -b TT_Daemon::Brodmann_area_18 -c TT_Daemon::Brodmann_area_19 -d TT_Daemon::Brodmann_area_37 -e TT_Daemon::Brodmann_area_7 -f TT_Daemon::Brodmann_area_32 -g TT_Daemon::Brodmann_area_24 -h TT_Daemon::Brodmann_area_40 -i TT_Daemon
by
Sabrina
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AFNI Message Board
Thank you for your help. I've since used a different approach that works and am no longer trying to use this way to analyze my data.
by
Sabrina
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AFNI Message Board
3dDeconvolve -xout -input scaled_allruns+orig -num_stimts 13 -stim_file 1 Sample_a.txt -stim_label 1 SmplTarg -stim_minlag 1 0 -stim_maxlag 1 3 -stim_nptr 1 1 -stim_file 2 nTAR1_a.txt -stim_label 2 NewTar1 -stim_minlag 2 0 -stim_maxlag 2 3 -stim_nptr 2 1 -stim_file 3 nTAR2_a.txt -stim_label 3 NewTar2 -stim_minlag 3 0 -stim_maxlag 3 3 -stim_nptr 3 1 -stim_file 4 nTAR3_a.txt -stim_label 4 NewTar3 -
by
Sabrina
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AFNI Message Board
afni_proc.py -subj_id NI25 -dsets run1+orig run2+orig run3+orig run4+orig -blocks tshift volreg blur mask scale regress -copy_anat anat+orig -do_block align tlrc -volreg_align_to last -volreg_align_e2a -volreg_tlrc_warp -blur_in_automask -regress_stim_times stimes.NT1.1D stimes.NT2.1D stimes.NT3.1D stimes.ND1.1D stimes.ND2.1D stimes.ND3.1D stimes.ST1.1D stimes.ST2.1D stimes.ST3.1D stimes.SD1.1D s
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Sabrina
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AFNI Message Board
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