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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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Results 121 - 136 of 136
Hi Afni experts,
I am looking to run ICA analysis on data previously processed with afni. I know I will have to make some modifications regarding how to analyze and needed guidance on one particular aspect regarding motion scrubbing.
Previously I would run through afni_proc.py and get a file of combined TRs to delete from extreme outliers and motion that I would incorporate at the end us
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AjaySK
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AFNI Message Board
Hi Rick,
I fixed the interpolation issue using the -final command so I think the only issue is regarding the centering of the voxels. I will try the new binaries and follow up with you this week. Thanks for the fix!
-Ajay
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AjaySK
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AFNI Message Board
Hi Rick,
It is possible that this was the one patient the tech pulled out to put the physio on so there was a shift in location. Unfortunately I was not there that day for the scan. I checked 3 files with 3dCM:
1) Resting state :
++ Oblique dataset:./EP_001.RS+orig.BRIK is 12.110529 degrees from plumb.
-1.69794 -24.4452 4.27884
2) T1 (raw):
++ Oblique dataset:EP_001.T1.nii is 10.193
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AjaySK
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AFNI Message Board
Hi Rick,
I am not sure if this also explains the issue I had regarding 3dAllineate/afni_proc.py/align_epi_anat. I would register the T1 to the EPI (far apart) and so during the initial alignment of centers the temporary file looks good. The centers matched the EPI and the T1 was centered in the window. However, no matter what option I tried (including supplying align centers with -pre_matr
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AjaySK
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AFNI Message Board
No problem Rick. I had a question for a subsequent step in the analysis.
When I aligned my anatomical to the EPI scan (they were far off and shifted) the alignment worked out great with afni_proc.py align block and I saved the transform. The one question I had is that my aligned anatomical brain is now in the lower right quadrant of the image as opposed to centered in the viewer (matches EPI
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AjaySK
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AFNI Message Board
Dear Afni experts,
I traced back the issue to an earlier command which was calling out the TR as opposed to the number of slices from the header information and passing the variable to McRetroTS.
-Ajay
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AjaySK
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AFNI Message Board
I uploaded the file as AjayKurani_McRetroTS which contains the puls.1D, resp.1D and oba.slibase.1D files in it.
Thanks,
Ajay
by
AjaySK
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AFNI Message Board
Hi Afni experts,
I am using McRetroTS for the first time and I got an error when processing the oba.slibase.1D file in afni_proc.py. I have 160 volumes with a TR=3s and I remove 4 TRs. Also my puls/resp sampling rate is 50 Hz. The scans are interleaved in +z direction and even #slices on a Siemens Trio, therefore alt+z2. Do you know what the error is related to and how to correct it? My
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AjaySK
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AFNI Message Board
Hi Daniel,
Thanks for the clarification. I will look into the post and see whats the best way to do this with the three different scans assuming the angles are different in order to minimize freesurfer processing (definitely takes long!). I will also try 3drefit as you suggested and post any solutions I get after more testing.
Thanks,
Ajay
by
AjaySK
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AFNI Message Board
Hi Peter,
I have 2 EPI scans (which may or may not have slightly differnet oblique angles from each other) and 1 T1 scan which has a different angle. I am using freesurfer for segmentaiton, skull stripping and normalization (not surface mapping at this time). I want to only have to process the freesurfer files once and then align the brain.mgz T1 and corresponding masks to the EPI scan as o
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AjaySK
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AFNI Message Board
Hi Daniel,
I had one additional question. If I have 1 T1 image and 2 EPI datasets and all with different oblique angles I wanted to find out the best way to use 3dWarp -card2oblique. I would not be able to use it on the original T1 image as this would force me to run freesurfer twice (since i'd need 2 copies of T1 to match the different oblique angles of the 2 EPI datasets). I had the
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AjaySK
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AFNI Message Board
Hi Daniel,
Thanks for explaining about the oblique data set sitting in a cardinal grid....this makes alot of sense now. The T1 after running 3dAllineate looks like it is in good alignment with the EPI. When I deobliqued the aligned image is when things looked severely out of alignment (which makes sense given what you said that I should not have to deoblique).
Just curious for 3dWarp -
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AjaySK
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AFNI Message Board
Hi Afni Experts,
I wanted to follow up with questions about oblique datasets. I have EPI and T1 scans that were both taken at slightly different oblique angles. I want to keep the EPI scan as is so that I minimize any steps that would alter the raw data (oblique angle 12.44). I have a T1 image which I processed through freesurfer and want to use 3dAllineate to move the anatomical scan to th
by
AjaySK
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AFNI Message Board
Hi Rick,
I uploaded the files so hope this helps. Goodluck.
Thanks,
Ajay
by
AjaySK
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AFNI Message Board
Dear Afni experts,
I wanted to use physio and B0 correction on my EPI scans for resting state analysis. I wanted to see if there are any implementations currently (or potentially in the future) for B0 correction within afni?
Now for the main quesiton: I wanted to verify the pipeline in terms of if you suggest motion correcton or slice timing first when using phsyio data/B0 correction.
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AjaySK
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AFNI Message Board
Hi Afni Experts:
I ran into an odd issue using code that I have used before. I used to use 3dcalc to combine GM/WM/CSF brain masks and subtract the saggital sinus mask out I created. I would then use the 3dmask_tool command to fill in any holes in the resulting file:
3dcalc -a mask_c123456.nii -b mask_c5.nii -expr a-b -prefix WB.nii
3dmask_tool -input WB.nii -dilate_input 2 -2 -fill_holes
by
AjaySK
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AFNI Message Board
Page 5 of 5
Pages: 12345