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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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Hi,
Can you help me to know about "how to read the .nii volume " using any high level language(I'm working in C) instead of reading it slide by slide. Any help in this regard would be highly appreciated.
by
Gunjan
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AFNI Message Board
Thanks Daniel,
But this is not what I was asking for. I mean I have say 181 2D slices of same width and height ( because I got these from slicing of a volume A) and I want to form a volume B from these slices. After stacking I want to preserve all the major properties (like orientation and slice thickness) in volume B.
by
Gunjan
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AFNI Message Board
Thanks Zhark :)
Can you please tell me a way so that I can stack my 2D slices without the orientation and thickness affected?
by
Gunjan
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AFNI Message Board
Hi All,
I am getting the below warning while performing skull stripping. How should I take it "
*+ WARNING: NO spatial transform (neither qform nor sform), in NIfTI file 'm000-stacks-m000-t1_icbm_normal_1mm_pn1_rf40-00001.nii'
Regards,
Gunjan
by
Gunjan
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AFNI Message Board
Thanks Ziad,
I need to perform a "set of noise removal algos" to each of the slices and then combine it as a volume.
Can you please help me in converting 2D slices into a 3D volume ?
These slices are obtained from a volume itself and after performing some operations ( change in pixel values by noise removal ) on each slice , these need to rejoin in order to form a volume without
by
Gunjan
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AFNI Message Board
Does "3dSkullStrip -input inputVolume.nii -prefix ss_mask.nii -mask_vol" perform any noise removal or bias field correction ?
If yes then what is the alternative in order to obtain only brain mask without noise removal and bias correction correction.
by
Gunjan
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AFNI Message Board
Hi Rick,
I think, this won't resolve the issue as in the AFNI generated mask, pixel values lying in brain portion decided by the AFNI people. How can I be sure that a particular pixel with a particular associated value is the brain pixel or the non-brain pixel. As, Gang told to take it as 0 and 1 but this way I'm able to obtain only the boundary of brain. I need the inside values as
by
Gunjan
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AFNI Message Board
When I used below code then mask is properly visible(not only the boundary).
cell_t binary( cell_t ft)
{
if(ft == 6)
ft=255;
else
ft=0;
return ft;
}
I used 6 because , after reading the image I found the largest pixel having value as 6. There are other values present as well like 2,4,1 etc.
My question is Did I process correctly? If not then how can I be sure that pixel values othe
by
Gunjan
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AFNI Message Board
I used the same information and tried to process the AFNI generated mask as below:
cell_t binary( cell_t ft)
{
if(ft == 1)
ft=255;
else
ft=0;
return ft;
}
But output is only showing the outline of the brain. I don't know why the file is not getting attached to this message.
by
Gunjan
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AFNI Message Board
I want to know the pixel values(0 or 255 or something else) of the generated binary mask because brain portion in slices is not visible in my system.
by
Gunjan
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AFNI Message Board
Hi,
output of 3dinfo -min -max a.nii is
0 11
Volume a.nii is downloaded from BrainWeb dataset.
I don't know how to set the path to abin so that I would no need to go abin directory everytime.
by
Gunjan
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AFNI Message Board
For few of my volumes it is showing :
The output dataset is a mask reflecting where voxels in the
input dataset lie in the brain.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip's -orig_vol option
or run the following command:
what does it mean while its giving mask.?
by
Gunjan
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AFNI Message Board
3dskullstrip command is ran but showimg the warning(text in red color). Other skull stripping algorithms are not showing such warning for the same input. Can you please help me in this.
I did not get the BRIK extension as well.
bibl04@BIBL04:~/abin$ ./3dSkullStrip -input a.nii -prefix ss_mask.nii -mask_vol
oo Warning 3dSkullStrip (SUMA_3dSkullStrip.c:1537):
Input dataset has a very
by
Gunjan
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AFNI Message Board
bibl04@BIBL04:~/abin$ ldd "$(which 3dSkullStrip)"
ldd: ./: not regular file
bibl04@BIBL04:~/abin$ ls /{,usr/{,local/}}lib*/libgsl*
ls: cannot access /lib*/libgsl*: No such file or directory
ls: cannot access /usr/lib*/libgsl*: No such file or directory
ls: cannot access /usr/local/lib*/libgsl*: No such file or directory
by
Gunjan
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AFNI Message Board
3dSkullStrip command is showing below error:
"3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory"
Output of ls:
bibl04@BIBL04:~/Desktop/BET/Data$ ls
subject05_t1w_p4.nii subject42_t1w_p4.nii subject48_t1w_p4.nii
subject06_t1w_p4.nii subject43_t1w_p4.nii subject49_t1w_p4.nii
subject18_t1w_p4.nii subjec
by
Gunjan
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AFNI Message Board
3dSkullStrip -input a.nii -prefix ss_mask.nii -mask_vol showing **ERROR: "can't open dataset a.nii".
I want to send the file I'm giving as input but here its not possible due to the big size.
by
Gunjan
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AFNI Message Board
Hello Sir,
Output of afni_system_check.py -check_all is:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.5.0-54-generic
version: #81~precise1-Ubuntu SMP Tue Jul 15 04:02:22 UTC 2014
distribution: Ubuntu 12.04 precise
number of CPUs: 8
apparent log
by
Gunjan
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AFNI Message Board
While setting up the path it is showing the error :
bash: syntax error near unexpected token `('
by
Gunjan
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AFNI Message Board
Hi,
I tried to used the 3dSkullStrip command using Ubuntu 12.04 terminal, in order to get the 3d brain surface as well as the binary brain mask but the "command not found "error mesage is being shown. I am using the BrainWeb data set and converted the data from .mnc to .nii format.
Can anyone help me in this ?
by
Gunjan
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AFNI Message Board
Hi,
It would really be appreciated if anyone could let me know the steps to extract brain from the nii volume.
by
Gunjan
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AFNI Message Board