Show all posts by user
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 151
Pages: 12345
Results 1 - 30 of 4524
Does this really mean the board will be read-only as of tonight?!?
What am I supposed to do until Monday?
Goodbye old board. <sniff!>
- rick
by
rick reynolds
-
AFNI Message Board
If motion registration has already been done, you certainly don't want to ask AFNI to do it a second time. But still include the motion parameters in the regression, and censoring as may be appropriate. It would be pretty bad if they performed motion correction but did not provide any estimates with the output data. It should be available somewhere.
- rick
by
rick reynolds
-
AFNI Message Board
Indeed, just track the follow_ROI dataset(s), and note EPI inputs. But ROI averages should come from just the volreg output (i.e. on the final grid). They do not get subjected to blurring, in particular.
- rick
by
rick reynolds
-
AFNI Message Board
Hi Philipp,
Pass the motion file using -regress_motion_file.
- rick
by
rick reynolds
-
AFNI Message Board
Yes, that is right. Just recall that the mask needs to be on the final (EPI) grid.
- rick
by
rick reynolds
-
AFNI Message Board
Hi Philipp,
ROI (average or multiple PC) regression can be done via -regress_ROI or -regress_ROI_PC, where masks are passed via either -anat_follower_ROI or -mask_import (or via the internal 3dSeg generation).
Example 11 shows use of -anat_follower_ROI (with FreeSurfer ROIs), which can then be applied with either -regress_ROI or -regress_ROI_PC. In this case, the ROIs start of in "ori
by
rick reynolds
-
AFNI Message Board
The only small point I might add is that adding "-radial_correlate_opts -polort 18" should have affected the @radial_correlate script as you hoped. There would be *2* -polort options in the command in the proc script, but yours would be later and therefore override the first (a subtle point).
But still, use the options Paul suggests.
A minor effect of this goes the opposite way t
by
rick reynolds
-
AFNI Message Board
Hi,
I do not believe there is such a tool in AFNI. The DICOM images come in varied formats and data types, and come after their own headers. While I have done a similar operation before, it was by:
- converting them to datasets
- applying the operation
- writing the raw data back into the DICOM file (after the header)
Since most software handles NIFTI images, would it be possible to
by
rick reynolds
-
AFNI Message Board
Hi Sally,
Thanks for that, it will be included with the next build!
- rick
P.S. We might make a macos_12 build, if you would be interested in testing it out.
P.P.S. Compiling is another option, and we are in the process of making that a little easier.
by
rick reynolds
-
AFNI Message Board
Hi Eddie,
We have a more compatible package for Rocky 8, with instructions and binaries:
https://github.com/afni/afni/blob/master/src/other_builds/OS_notes.linux_rocky_8.txt
https://afni.nimh.nih.gov/pub/dist/tgz/linux_rocky_8.tgz
Note that those instructions are for a build machine. You should be able to remove -devel from those package names.
But other than the admin instructions, y
by
rick reynolds
-
AFNI Message Board
It is hard to say what is causing that failure, so would you try a couple of things?
1. Try it without the quotes:
xvfb-run -a vglrun -d egl 3dTcat \
-prefix Temp.nii \
Zero_dataset.nii \
$file_paths
2. Try it from the subdirectory. Forget the ROI order, this is just a test...
cd /project/..........THAT_PATH_TO.../Yeo7N_1000ribbon
xvfb-run -a vglrun -d egl 3dTcat -prefix Temp.nii Zero
by
rick reynolds
-
AFNI Message Board
Hi Maya,
You could run afni_proc.py on the EPI datasets, just telling it to do the scale and regress blocks:
afni_proc.py -subj_id phant.SR \
-dsets phantom*.nii \
-blocks scale regress \
-tcat_remove_first_trs 2
To get more QC out, include the volreg block, even if it should not do much.
Also, here I
by
rick reynolds
-
AFNI Message Board
Just to follow up, we resolved this by fixing the .cshrc file.
- rick
by
rick reynolds
-
AFNI Message Board
Okay, I hope it works out well. Please feel free to send me the Dimon "details" files.
- rick
by
rick reynolds
-
AFNI Message Board
Hi Kayla,
Then I am a little confused why the "bash SCRIPT" method failed. I will send you personal email to look more closely.
But just as a sanity check, in the script, before afni is run, can you add a similar line:
echo $DYLD_LIBRARY_PATH
Thanks,
- rick
by
rick reynolds
-
AFNI Message Board
If you have the original DICOM files, then Dimon has different options for sorting via -dicom_org.
If you try that, start by including "-save_details DET", and feel free to send me the DET* text files via email.
But I don't actually see why you would want the files in the order slice0(TE0, TE1,..., TE15), slice1(TE0, TE1,..., TE15),...
To be sure, currently the first apparen
by
rick reynolds
-
AFNI Message Board
Cool, and to be sure, what is the output from
echo $0
echo $DYLD_LIBRARY_PATH
Thanks,
- rick
by
rick reynolds
-
AFNI Message Board
That is interesting. If it is failing in bash, then maybe there is a discrepancy between whatever libXp is being shipped with FreeSurfer and the one that is otherwise on your system. But to be sure, let's forget doing it from a script for now. Since your login shell is bash, just try running commands by hand.
1. from your bash terminal, can you start afni?
2. assuming that fails, woul
by
rick reynolds
-
AFNI Message Board
Hi Kayla,
Your script is given as SOMETHING.sh. If you actually use 'sh' to run it, those DYLD variables will probably not be set in that sub-shell. Does that apply, or is that script run via bash?
Would you specify exactly how you execute the DWI_do_01_QC.sh script?
Thanks,
- rick
by
rick reynolds
-
AFNI Message Board
It looks like one of the NN responses is being totally censored out (which is not so odd). That is one difficulty with IM, there is a reasonable chance that censoring will cover all of the time points for at least one event response, giving you one or more all-zero regressors. To have it proceed, it is necessary to include at least the warned about -GOFORIT level (in this case, 3). But some su
by
rick reynolds
-
AFNI Message Board
Hi Jeremy,
Is this in DICOM format or NIFTI (or AFNI)? It seems like you are starting with a 4D dataset that needs to have the slices transposed. Is that right? Or do you want a set of individual slice files?
Thanks,
- rick
by
rick reynolds
-
AFNI Message Board
Hmmm, the plot thickens. Those commands work for me.
And I cannot test on my home mac right now. Complications...
Does this work for you?
head ${crazypath}/I1000000
- rick
by
rick reynolds
-
AFNI Message Board
Hey Z,
Is that with a long path or just a long /-less name?
A long path+name seems to work for me. A long directory-less name actually fails at the shell, with the error: File name too long
I cannot use 'touch or 'mv' for example, to create such a file.
- rick
by
rick reynolds
-
AFNI Message Board
Oh, thanks for the output. I did not notice, but your commands include -regress_reml_exec and -regress_3dD_stop, so 3dDeconvolve is not being used to perform the regression. And unfortunately, 3dREMLfit is not able to create iresp output, that only works in 3dDeconvolve which is not being used.
You *can* use 3dbucket or 3dTcat to extract the betas of interest from the 3dREMLfit output. It i
by
rick reynolds
-
AFNI Message Board
Hi Zhengchen,
That is right, the timing does not need to be rounded, so using the 0.1 s resolution sounds good.
Yes, there will not be much difference between BLOCK(0.2,1) and BLOCK(1,1), though the peak of the latter will be close to that 0.8 s difference.
What is a typical range of durations?
That is right, if the median duration is about 0.2s, using dmUBLOCK(-0.2) would be reasonab
by
rick reynolds
-
AFNI Message Board
Hi Zhengchen,
There should be a dataset with a name starting with iresp_Rsw. If you would like, please send direct email (click on my name) with the text output from running 3dDeconvolve, or maybe just the output.proc.SUBJECT file.
- rick
by
rick reynolds
-
AFNI Message Board
Hi Philipp,
The -xbox/-dbox/-nbox options take x y z coordinates, which without ranges have nothing to do with the voxel sizes.
However, if you want the -xbox to be a range of voxels, let's say of size +/- 3mm, and centered at coordinate 10,20,30, for example (to include 27 voxels around that central point), you could use ranges of -/+ 3mm around each central coordinate. I will leave
by
rick reynolds
-
AFNI Message Board
Hello,
The error messages, particularly the one suggesting a dependent metafor package is no longer available for 3.6, is concerning. Perhaps that means the R 3.6 dependency on the 10.12 binaries is no longer an option.
We will investigate this a bit more.
Thanks,
- rick
by
rick reynolds
-
AFNI Message Board
Hello,
At a glance, that looks okay, because while the shell fails to match it, an AFNI program could (via the AFNI library).
But since you are using a wildcard, it must exactly match a file name on disk. So try adding .HEAD at the end of the REML+orig dataset name.
Of course, adding .HEAD will probably mean that the shell will then succeed in matching it in the 3dUndump command, and then
by
rick reynolds
-
AFNI Message Board
Page 1 of 151
Pages: 12345