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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
I'm glad you got it worked out. The dset1,2 terminology is a shortcut for a couple things, but mostly the effect here is probably from a change in the default cost function to lpa.
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Daniel Glen
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AFNI Message Board
Partial images can be particularly difficult. If the data starts out this far apart, it seems there is something off in the coordinates. Try "-giant_move" to overcome that and allow movement a long distance. Cost functions like lpc+ZZ, lpc and nmi may be used too (-cost ...). There are options for partial coverage, but that assumes movement mostly within the planes of the acquisition, a
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Daniel Glen
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AFNI Message Board
Adding a little more to this -
1. Cost function. Consider nmi in addition to the lpc and lpc+ZZ cost functions for differing tissue intensities like this.
2. Manual masking. Masking the data by hand with a simple sphere might be a good initial mask particularly if you have lots of other material, neck, shoulders,....
3. CT. If you happen to have a CT volume, you could compute a mask from tha
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Daniel Glen
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AFNI Message Board
Aside from Paul's sage advice, another important point is that RAI is not really the "default" in AFNI. There is no default, so you could use any orientation.
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Daniel Glen
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AFNI Message Board
That sounds fine to me. Changing the actual coordinates would change the reference system, but if you were creating a new atlas, that might be a better way. For the zeropad idea, you can do this a bit more automatically with 3dAutobox using a brain mask and then 3dZeropad with the autoboxed brain mask as the master. Add a few slices around to allow for alignment of other datasets.
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Daniel Glen
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AFNI Message Board
That shows a disagreement between the DICOM header fields that sometimes seen in Siemens mosaic files. It usually won't be too important if you align the EPI and anatomical data. You can always use the oblique information from the mosaic with the "-use_obl_origin" for Dimon.
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Daniel Glen
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AFNI Message Board
It has been a very long time since we looked at that program, but we're happy to help. The model we used was a 2-compartment, 3 parameter model. The Expr2 model option is probably too simple for that. The use of that model required some preprocessing to transform the data given optional relaxivity maps from dual flip angles, an input vascular time series (estimated from a sagittal sinus vein
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Daniel Glen
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AFNI Message Board
There is also a small issue with the -j option. The make doesn't quite parallelize, but it usually works the second time through. Anyway, I'd skip that for this test.
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Daniel Glen
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AFNI Message Board
Adding a tiny bit more to Rick's usual sage advice, R should be installed first before the build.
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Daniel Glen
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AFNI Message Board
That's right. Resample the dataset to a temporary master dataset with the coordinate order you have. Only a single subbrick volume dataset is needed. You could reorder the coordinates too, but it's easier this way.
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Daniel Glen
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AFNI Message Board
I'm using that version now, and I think it's working well. The only exception I have found is the bug in Xquartz that shows up specifically with volume rendering in suma, but that's been in the last few versions too.
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Daniel Glen
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AFNI Message Board
One point about the coordinates (one that I should probably fix so that this point doesn't need to be made) is 3dUndump always reads in coordinates in the "master" dataset's storage orientation. So if you want to use RAI coordinates, you can create a dataset in RAI storage orientation with "3dresample -orient RAI"; likewise, for LPI order, the most commonly used orde
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Daniel Glen
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AFNI Message Board
Paul's solutions looks pretty good to me, but for 5000 ROIs, it might be a little slow, but that might not be too bad. We have something a little like this inside our Draw Dataset plugin - line propagation and then ROI filling, but it's not exposed in a separate function. For reference, I think the line propagation is done in AFNI_3d_linefill() in afni_receive.c and DRAW_2dfiller in plu
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Daniel Glen
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AFNI Message Board
See this previous post for setting shell paths from inside Matlab.
https://afni.nimh.nih.gov/afni/community/board/read.php?1,158256,158279
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Daniel Glen
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AFNI Message Board
Try updating XQuartz to the latest version (now 2.8.2) and restart.
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Daniel Glen
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AFNI Message Board
For datasets that have an sform or qform code = 2, AFNI_NIFTI_VIEW may be set to either orig or tlrc. Add that to your ~/.afnirc file (possibly with "@AfniEnv -set AFNI_NIFTI_VIEW orig").
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Daniel Glen
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AFNI Message Board
Hi Chris,
If the template and the subject intensities are completely or partially reversed (CSF-dark in one and light in the other), then lpc, lpc+ZZ or nmi are usually good choices. If the sizes are very different, then the -supersize option might help too. Otherwise, I am considering adding a unifize option that might call 3dUnifize or 3dLocalUnifize that could help for some datasets. You ca
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Daniel Glen
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AFNI Message Board
Here is a little different variation that works based on euclidean distance instead of distance along the A-P axis.
https://afni.nimh.nih.gov/afni/community/board/read.php?1,157456,157474#msg-157474
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Daniel Glen
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AFNI Message Board
You can also get a list of the unique output values in a table
3dRank -prefix testrank -input myatlas_or_roi_dset.nii.gz
or
3dmerge -1rank -prefix testrankmerge myatlas_or_roi_dset.nii.gz
cat testrank.rankmap.1D
#Rank Map (361 unique values)
#Col. 0: Rank
#Col. 1: Input Dset Value
0 0
1 1
2 2
3 3
4 4
...
360 1180
You can also loop in a script across individual v
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Daniel Glen
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AFNI Message Board
How are you mapping the data to the surface? If you are using the default afni-suma communications, then you will only get the intersections of the surface with the voxels of the volume. That will often leave holes if the mask bends even just a little away from the volume. If you are doing this interactively, you can use the Vol2surf plugin to adjust how that's done and allow for the mode/me
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Daniel Glen
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AFNI Message Board
You could use the -singletonA option for each subject versus the subject's group.
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Daniel Glen
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AFNI Message Board
align_epi_anat.py has -partial_... options that might help. Still, it can be difficult depending on how much spatial structure there is in the anatomical datasets. It's usually best to acquire partial coverage datasets with a full brain dataset, and then use alignment of that full brain dataset to pull the partial one as a kind of follower dataset.
There was a recent thread here too on th
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Daniel Glen
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AFNI Message Board
Hi Stefano,
Hmm, it seems you are right about this. I haven't tracked this down to where it happens inside 3dSkullstrip, but it's not too bad a workaround using the recommended code for masking the original volume that comes at the end of its terminal output:
3dcalc -a anat_oblique.nii.gz -b anat_ns_notoblique.nii.gz -expr 'a*step(b)' -prefix anat_ns_oblique.nii.gz
The
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Daniel Glen
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AFNI Message Board
If you are using only an affine transformation, then you can use Vecwarp to transform lists of coordinates.
https://afni.nimh.nih.gov/afni/community/board/read.php?1,158095,158098#msg-158098
https://afni.nimh.nih.gov/afni/community/board/read.php?1,146048,146181#msg-146181
You can load these tags in from a new file with those new coordinates, or put spheres down instead of "tags"
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Daniel Glen
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AFNI Message Board
You can plot the motion parameters with "1dplot -volreg" to see their magnitudes. If motion is small enough, you may not see a difference at all. Of course, that also depends on the visualization software.
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Daniel Glen
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AFNI Message Board
The missing label is a very old issue that goes back to the original atlas, and I had asked the authors of the atlas about that along with a variety of other missing information. This missing region was noted by another AFNI user a few years ago. It appears to be "Cerebellar Vermis (10)" for the index value of 116. I don't have confirmation for that, but I can update the atlas with
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Daniel Glen
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AFNI Message Board
If you can reproduce this with just a single script, that's great. The problem may be intermittent based on network traffic and file server activity. I would try both increases and decreases in the samba cache. This was from a quick google search :
# Cache data before flushing to disk:
write cache size = 2097152
min receivefile size = 16384
getwd cache = true
https://coderwall
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Daniel Glen
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AFNI Message Board
Since this is smb, try adjusting the buffer size in smb.conf. This was still in a single script that did things sequentially, and 3dTstat was one of the steps?
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Daniel Glen
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AFNI Message Board
AFNI format datasets are opened and closed with popen and pclose, but NIFTI format datasets are handled with the znzlib, which uses the zlib function gzopen, gzclose and a variety of gz... functions for writing. I suspect there is some odd buffering problem on the distributed file system that might be handled with a combination of flush and sleeps before and after gzclose. That's all in one
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Daniel Glen
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AFNI Message Board