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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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Thanks, it worked!
One more question: Is there anyway to have a discrete set of colors instead of continuous ones? My ROI #1 gets a mixed color of black (I guess default color for index 0) and the color I set for the index 1 in my color palette. When I click the " # " below the color bar, I see values up to 20 and then **, so wondering whether there is any way I can set it to certain
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suhyun84
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AFNI Message Board
Dear staffs,
I'm making a color palette using my own color lookup table to color my ROIs as I want. I made a .txt file containing index, string label, R,G,B,Alpha values for each row for each ROI. When I use MakeColorMap to convert this file into .pal , i got error messages like below. What did I do wrong? I attached a screenshot showing the error messages in the terminal window and my te
by
suhyun84
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AFNI Message Board
Hi, I'm trying to change my ROI volume data to surface dset. Is it correct to use 3dVol2Surf in this case? If so, should I put my volume ROI file as input for -grid_parent or -map_func (or -mask?)?
Eventually what I would like to do is to visualize only the boundaries (contours) of the ROIs on the surface..
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suhyun84
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AFNI Message Board
Hi AFNI experts,
Is there any way in AFNI/SUMA to visualize only the edges of ROIs, without filling inside each ROI?
Thanks in advance,
Soo Hyun
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suhyun84
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AFNI Message Board
"apple+ctrl+r" also increases the oversampling factor. I also tried "ctrl+shift+r", which actually turned on/off the disk recording of image, as if it's normal "ctrl+r". So in my terminal:
"r" = "alt+r" = "ctrl+r" = "apple+ctrl+r": changes the oversampling factor, like normal "alt+r"
"ctrl+shift+r":
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suhyun84
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AFNI Message Board
Okay, thank you for your prompt help. I'll try driver scripts. It's kind of interesting that both "r" and "Ctrl+r" behave as if "Alt+r", i.e. increasing image oversampling factor. I'll check whether anything I should change from the Linux machine side too. Anyway, thanks for your help again!
Best,
Soo Hyun
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suhyun84
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AFNI Message Board
It worked: "SUMA_Recordings" directory was created with one image inside.
by
suhyun84
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AFNI Message Board
The AFNI version I have is AFNI_20.1.10 'Otho' (linux_openmp_64: May 26 2020). I also found we don't have Netpbm installed, but I don't think it should matter..
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suhyun84
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AFNI Message Board
I don't think so- I'm using Linux workstation via virtual machine from Mac OS using Mac keyboard, but the number keys in "number pad" in my keyboards presses as "numbers", so I don't think the numlock is on.
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suhyun84
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AFNI Message Board
"ctrl+r" also changes the oversampling in the same way as "r".
by
suhyun84
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AFNI Message Board
Hi,
Somehow the shortcut for capturing single image, "r", doesn't work in SUMA. Other keys such as shift+r for recording works fine, but when I press "r", it just changes "oversampling" to 2 -> 3 -> 4 -> 1 -> 2... and so on (see the attached screenshot). Any idea why it's happening? I'm running AFNI & SUMA on Linux.
Thanks,
Soo
by
suhyun84
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AFNI Message Board
Thanks for the prompt reply with detailed help! It worked well and I could have labels on.
I have one more question regarding ROIs generated from SUMA. Is there any way to modify the volumetric dataset of surface-generated ROIs in AFNI? In other words, in your above example with three_rois.lh.s2v.roi+orig, whether you can open three_rois.lh.s2v.roi+orig.BRIK in the AFNI and modify each ROIs us
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suhyun84
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AFNI Message Board
Hi, I have a question about keeping the labels for ROIs that I created in SUMA. After I created and saved a set of ROIs on the surface using SUMA (with NIML and All options), I used ROI2dataset and 3dSurf2Vol to convert them into volume coords. I needed to open it in Matlab using "BrikLoad" to apply the ROIs to my data matrix in Matlab. Everything looked alright except I don't have
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suhyun84
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AFNI Message Board
The output of "afni -ver" is this: Precompiled binary macosx_10.7_Intel_64: Jan 20 2017 (Version AFNI_17.0.02)
Is it related to freesurfer installation or something? I can use MakeColorMap command with -fn option, but only this type of color look up table doesn't work.
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suhyun84
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AFNI Message Board
Hi,
I made my own color lookup table like text file (freesurfer style) and tried MakeColorMap. It failed with the error messages like below. What would be the problem?
#label String_label R G B A
1 Cluster1 205 62 78 255
2 Cluster2 245 245 245 255
3 Cluster3 205 62 78 255
4 Cluster4 120 18 134 255
5 Cluster5 196 58 250 255
6 Cluster6 0 148 0 255
7 Cluste
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suhyun84
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AFNI Message Board
Hi, I am running AFNI/SUMA in OS X 10.11.6 (El Capitan). I tried to update AFNI/SUMA by running @update.afni.binaries -d in terminal, it failed with timeout errors. Below is what I got as error message. What should I do? FYI, I installed AFNI a couple of years ago, probably under OS X 10.8 (Mountain Lion). This was first time that I tried update in a long time (you can see the current version I
by
suhyun84
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AFNI Message Board