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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
Page 1 of 2
Pages: 12
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Thanks. That seems to work. Thank you again very much for your time into this. I am very appreciative
by
ebaldelo
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AFNI Message Board
I thought it worth starting a new reply for this:
I took a smaller subset and methodically edited the different values. It appears column 4, roll, value appeared to be the culprit. Below are values from a dfile_VolReg2_aff12.1D file:
-0.0288 -0.124 -0.005 0.8544 0.0083 -0.0323 0 0 0 0 0 0
-0.0254 -0.1439 -0.002 0.8848 0.0439 -0.0921 0 0 0 0 0 0
0.1401 -0.7076 0.0146 4.8042 0.101 0.1251
by
ebaldelo
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AFNI Message Board
Below is my command and a few things worth mentioning:
1) Unregistered Data is: $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box+orig
2) Data is despiked before registration: $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box.DS+orig
3dvolreg \
-overwrite \
-prefix $AnimalID/$FolderID/${AnimalID}_${FolderID}.DS.BoxReg \
-base $AnimalID/$FolderID/${AnimalID}_${FolderID}.Box.Mean+orig[0]
by
ebaldelo
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AFNI Message Board
1) This is the end of the output:
++ update needed, installing...
++ downloading full package: curl -O -f macos_10.12_local.tgz ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 975M 100 975M 0 0 16.6M 0 0:00:58 0:00:58 --:--:-- 17.5M
++ extracting packag
by
ebaldelo
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AFNI Message Board
I don't understand why either. It's very strange. Here's the output:
>>tcsh ~/abin.corrupt/@update.afni.binaries -bindir ~/abin -package macos_10.12_local -defaults
/Users/ebaldelo/abin.corrupt/@update.afni.binaries: No such file or directory.
Here's this if it's worth knowning:
>> ls -l ~/abin*
/Users/ebaldelo/abin:
total 0
drwxr-xr-x 10 e
by
ebaldelo
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AFNI Message Board
Just tried that sequence and now I get this:
>> @update.afni.binaries -defaults
-bash: /Users/ebaldelo/abin/@update.afni.binaries: No such file or directory
here's this if it's helpful:
>> ls -al /Users/ebaldelo/abin/
total 0
drwxr-xr-x 10 ebaldelo staff 320 Mar 2 11:38 .
drwxr-xr-x@ 134 ebaldelo staff 4288 Mar 2 11:38 ..
drwxr-xr-x 6 ebaldelo
by
ebaldelo
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AFNI Message Board
Output:
>> ls -l ~/abin/afnipy/lib_afni1D.py
-rw-r--r-- 1 20892 staff 152834 Aug 19 2020 /Users/ebaldelo/abin/afnipy/lib_afni1D.py
I really thought I did '@update.afni.binaries -defaults' sometime last year. Either way... just tried it. and after downloading some files and extracting I start seeing a lot of 'Permission Denied', e.g:
-- running @update.af
by
ebaldelo
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AFNI Message Board
Output:
>> find ~/abin/ -name lib_afni1D.py
/Users/ebaldelo/abin//afnipy/lib_afni1D.py
>> grep g_1D_write_styles ~/abin/afnipy/lib_afni1D.py
>> echo pypath = $PYTHONPATH
pypath =
I also tried:
>> grep g_1D_write_styles /Users/ebaldelo/abin//afnipy/lib_afni1D.py
>> echo pypath = $PYTHONPATH
pypath =
1) Weird to me that in the path to 'lib_afni
by
ebaldelo
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AFNI Message Board
Hi Rick,
Thank you very much for your help with this. I unfortunately ran into a likely unrelated error when attempting to run the below.
1d_tool.py -infile $AnimalID/$FolderID/dfile_VolReg2.1D -volreg2allineate -write $AnimalID/$FolderID/dfile_VolReg2_aff12.1D
I just tried to run '1d_tool.py' and get the same error:
>> 1d_tool.py
Traceback (most recent call last):
by
ebaldelo
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AFNI Message Board
Hello
I am trying to use the output from 3dvolreg to adjust a data set using 3dAllineate -1Dparam_apply.
Reading the program help file: 3dvolreg outputs:
roll = rotation about the I-S axis }
pitch = rotation about the R-L axis } degrees CCW
yaw = rotation about the A-P axis }
dS = displacement in the Superior direction }
dL = displacement in the Left direction } mm
dP =
by
ebaldelo
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AFNI Message Board
It may have been an issue with the mask I was using. I just re-did the whole processing and it appears to be working now...
by
ebaldelo
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AFNI Message Board
Hello, I got the below error using the below code for 3dvolreg. This code was just working last week. So not sure what has happened/changed since. I even re-tried it on a data set that I used it with previously and got the same message. I use the code in a '.sh' file in case it's worth knowing but copying/using the code directly doesn't seem to change anything.
Thank you in
by
ebaldelo
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AFNI Message Board
Hello,
I keep getting the following error:
> 1dBandpass \
> -dt 0.150 \
> -nodetrend \
> 0.7 1.0 \
> ROIdump.1D \
> > ROIdump.BPresp.1D
*+ WARNING: bandpass: fbot=0.7 and ftop=1 too close ==> jbot=1 jtop=2
*+ WARNING: -- ignoring bandpass filter
+ bandpass: ntime=9 nFFT=10 dt=0.15 dFreq=0.666667 Nyquist=3.33333 passband indexes=0..4
+ -- remove mean
by
ebaldelo
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AFNI Message Board
Hi Daniel,
Thank you again very much for your time into this. I ran into an error running the part for '3dClusterize':
** FATAL ERROR: Hey, you need to put in threshold type/value!For example, '-2sided ...', '-1sided ...', etc.
*EDIT* Based off values in '3dcalc', i used the following and seemed to resolve the error. Would still be interested to he
by
ebaldelo
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AFNI Message Board
Sorry, I updated it. I do use the following option:
-warp shift_rotate \
by
ebaldelo
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AFNI Message Board
Hi Daniel,
Yes I seem to be a bit stuck. I just chose the 5th sub-brik b/c it had good contrast in the time series. Not really because it was off.
I couldn't get anywhere positive with align_epi_anat. I went back to 3dAllineate. I've been methodically using different iterations of parameters. This is what I've lately come up with as a set of parameters that improves the regi
by
ebaldelo
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AFNI Message Board
Hi Daniel,
Thank you for your input. I have a follow up question. I also watched your video online as a reference (https://cbmm.mit.edu/video/09-alignment-and-atlases-part-1-2).
Questions pertaining my use: I want to register the EPI data set to say it's 5th brik. I wasn't originally trying to register it to an anatomical set. Would the following code be appropriate?
align_ep
by
ebaldelo
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AFNI Message Board
Thanks for the tip. I was just in the middle of doing that. I think it may have improved it a bit. But I am curious how zero values might affect registration in a masked data set (to ensure clarity, by this I mean values inside of mask remain their value and outside of mask becomes zero). So, If a large part of the image is masked (set to zero), then would the registration algorithm try to align
by
ebaldelo
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AFNI Message Board
I thought it was worth clarifying, the data set is a few non-sequential 2D images. So felt 2D registration was more appropriate than using 3dvolreg. I referenced the discussion below to guide my choice to start this problem but the registration hasn't come out well at all. I've tried a few iterations tampering with the default values in 3dAllineate, but to no avail. My hope/thought is
by
ebaldelo
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AFNI Message Board
Hi All,
Hoping to find help with strategies in registering a time series of abdomen images. Respiratory motion is a bit tricky since all organs don't move exactly uniformly. I'm mostly interested in registering just one organ. So willing to use a mask with the base image but wasn't sure how to do that in 3dAllineate. I tried '-source_mask' but it completely threw off t
by
ebaldelo
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AFNI Message Board
Hi Daniel,
Thank you so much for your input on this. That is very helpful and what you suggest is exactly my desire. A last question on implementing it; how do you shift time series? I've gone through some documentation (e.g. ) or even with the even/odd topic, and it hasn't become apparent to me the command to shift a time series by one or n-number of steps? Any additional help with
by
ebaldelo
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AFNI Message Board
After reading a bit more of documentation it looks like '3dTshift' does this a bit with the '-voxshift fset' option. But requires an input data set. I'm curious if there are any other options to help determine this input option based on my above request. Any help is much appreciated. Thank you!
Cheers,
Edwin
by
ebaldelo
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AFNI Message Board
Hi All,
Another perhaps simple question: Is there a way to account for potential phase offsets during correlation? I guess what I have in my mind is:
- Circular shift each voxel time series until a maximum is reached for the correlation coefficient.
And an output of the max corr. coeff. with the offset phase shift would be great. Tried to do some quick searches in the board and couldn
by
ebaldelo
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AFNI Message Board
Ah, thank you for the link! I do very much appreciate that.
All the best!
Edwin
by
ebaldelo
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AFNI Message Board
I just figured out a way to do it:
>> 3dcalc -a epi_r1+'orig[0..(2)]' -b epi_r1+'orig[1..(2)]' -expr 'a+b' -prefix rm_3dcalc_sum2.nii.gz -overwrite
I might eventually want to sum ever 3 or 4 points together which I can add variables 'c' and 'd' and the adjusted above notation to do it. But if there's any more simple way to do it,
by
ebaldelo
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AFNI Message Board
Hi Daniel,
Thank you very much for answering this! I have a question about the 3dcalc operation:
I don't to repeat indices if they've already been summed. e.g. I want to only sum points 1 & 2, then 3 &4, 5& 6, and so on. Not 1 & 2, then 2&3, then 3&4, etc. as is done in the above setting. Thus my new data set would have a reduced time length of n_t/2 where
by
ebaldelo
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AFNI Message Board
Hi All,
I'm trying to perform a 'moving accumulation' (the best descriptor I can think of at the moment). I think similar to '3dcalc -accumulate' but I want to do this discretely. For example, I would like to sum every two values along time. And repeat the calculation for all 3D. In matlab, the most simple, equivalent command I could think of for a single timeseries wa
by
ebaldelo
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AFNI Message Board
Huzzah! It works on mine as well. I would like to extend my sincerest gratitude for all the help with this. I'm sure it may be something small but it is super helpful for me with analysis. Thank you so much!!
by
ebaldelo
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AFNI Message Board
Hi Paul,
Thank you. So I did the update and am looking at it now. Unfortunately, it still doesn't seem to work. Does it work properly on your terminal? Unless the build hasn't finished yet and thus isn't the correct updated version...
Cheers,
Edwin
by
ebaldelo
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AFNI Message Board
No worries! Thanks so much for looking into it. Very grateful and look forward to the next build. Haha, no doubt the complexity. All the best!
by
ebaldelo
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AFNI Message Board
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Pages: 12