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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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Hello,
I have been using SSWarper for skull-stripping and spatial transformation. This method worked find on most of the cases (24 out of 27), but 3 data sets didn't produce satisfactory results with skulls being not fully removed (see the attached). Since I have a small sample, I don't want to exclude these 3 cases from data analysis. Can you make a suggestion for an alternative met
by
cooldesert
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AFNI Message Board
Hello Rick,
The original voxel size is 3mm, not 1mm. When I reviewed original EPI data over anatomical data that was skull-stripped and transformed to standard space in AFNI, it looked fine. However, after applying align_epi_anat.py, EPI data didn't overlap with anatomical data at all (see attached). I tried the giant_move option, but this didn't make any difference, either. So I gue
by
cooldesert
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AFNI Message Board
Sorry! I must have misread your previous message. Here is the output.
As for the data size, I previously used 3dresample to change orientation, which changed the grid and thus file size. I didn't use it this time, and the whole folder size is about 7BG. FYI.
sungjin@SMHCAS211AL01:~/fMRI/CGE/265001.s1.results.v1$ ls -lh pb0*BRIK*
-rw-r--r-- 1 sungjin sungjin 50M Oct 26 12:44 pb00.2650
by
cooldesert
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AFNI Message Board
A technician came out and replaced old RAM with new ones. My machine seems to be working fine as I notice the difference in processing speed.
However, when I ran my script again, I got an error message as follows:
*** failure while opening brick file ./pb05.265001.r02.scale+tlrc.BRIK - do you have permission?
*** Unix error message: Cannot allocate memory
** Memory usage: chunks=6464 byt
by
cooldesert
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AFNI Message Board
Hello Rick,
I am sorry that I already deleted the results folder because the folder size is very big (over 150GB), and I had to free up the disc space for other operation. Now that I have ran the script again, the process was killed during warping this time. I copy the output file below. Could this be a hardware problem as I also notice that this Linux machine was getting noticeably slow when
by
cooldesert
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AFNI Message Board
Whenever I have an oblique warning, the obliquity is about 1 degree or even less, and I want to ask if I need to bother with deobliquing in this case? I attach screenshots of raw EPI data superimposed on raw anatomical data, and if you can make a suggestion, that would be nice.
The EPI voxel size is 3x3x4mm, and since I don't know why you mean by "afni_proc.py command", I attac
by
cooldesert
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AFNI Message Board
Hello pt,
It sounds like you suggest to use 3dwarp and I am re-running my script. I am also using an Intel Core i-5 LInux desktop with 12gb memory, so I don't think I am underpowered, right?
Sungjin
by
cooldesert
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AFNI Message Board
Hello pt,
Data consist of 6 blocks, and each block has either 150 or 180 time points. Do you this these are too many? I also want to let you know that I kept getting a warning that the data are oblique. So I used to use 3dwarp, but recently a colleague of mine suggested to use 3drefit, which made the data plumb. This is the only change that I made, and after this change, I got this "memor
by
cooldesert
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AFNI Message Board
Hello,
I ran my scrip that I created using proc.py, and it keeps giving me a "current memory mallocated" error. Below is part of the output and I also attach my script.
Sungjin
3dDeconvolve -input pb05.265003.r01.scale+tlrc.HEAD pb05.265003.r02.scale+tlrc.HEAD pb05.265003.r03.scale+tlrc.HEAD pb05.265003.r04.scale+tlrc.HEAD pb05.265003.r05.scale+tlrc.HEAD pb05.265003.r06.scale
by
cooldesert
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AFNI Message Board
Hello pt,
As you suggest, I used SSwarper for skulstripping and alignment. I found significant improvement in the alignment of anatomical data to a standard template. However, EPI to ANA alignment is still poor. I also notice that the "Check: statistics vols" no longer shows up on my QC report. Can you provide further advice?
afni_proc.py -subj_id $subj
by
cooldesert
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AFNI Message Board
Hello pt,
Thanks for your suggestions. I have a question about using SSwarper. In my original script, I used align_epi_anat.py and @auto_tlrc for skull-stripping and aligning anatomical data to standard space as you can see below.
# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new an
by
cooldesert
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AFNI Message Board
Hello,
I am new to AfNI, and I created a script using uber_subjec.py. I ran this script on 10 samples, and 8 out of 10 showed a similar big mismatch between anatomical and EPI data. After checking the attached QC report, can you suggest how should I change my script? If you have suggestion for other than alignment, that would be great as well! Thanks.
Sungjin
by
cooldesert
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AFNI Message Board
Hello Pt,
You are right. I forgot to install the VcXsrv server, and after the installation, both AFNI and suma are working fine. Thanks for your help!
Sungjin
by
cooldesert
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AFNI Message Board
After running the command, I see ":0.0" ( 0 is a zero).
Sungjin
by
cooldesert
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AFNI Message Board
Hello Pt,
I followed your instruction by running the commands and restarting the Ubuntu terminal, but I still get the same error message. Can you make other suggestions?
Sungjin
by
cooldesert
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AFNI Message Board
Hello,
I have been following the instruction to install AFNI. When I tried to launch the AFNI GUI by running the "afni" command, I get an error message. Please check the attached screenshots and share your advice on the next step. Thanks.
by
cooldesert
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AFNI Message Board