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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
Hmm... are you sure this is the first error? It looks like either things aren't getting built, or they're not where "make install" expects them to be, or /Users/admin/abin doesn't exist for some reason (though I would have expected "make install" to create it...).
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Isaac Schwabacher
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AFNI Message Board
This is most likely a scaling issue. IIRC, by default WriteBrik writes its output as 16-bit integers without scaling, so values between 0 and 1 will be written as either 0 or 1. If you add a .Scale field with value 1 to the Opt struct, the data will be scaled to fit the range of 16-bit representable values.
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Isaac Schwabacher
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AFNI Message Board
I suspect your problem is that there's no whitespace between your lines. Which is to say, when you write this: -dset 1 1 1 '3dcalc(...)'\
-dset 1 2 1 '3dcalc(...)' the shell is removing the backslash-newline pair to get this: -dset 1 1 1 '3dcalc(...)'-dset 1 2 1 '3dcalc(...)'
+----------------+
all one word If this is ind
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Isaac Schwabacher
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AFNI Message Board
Check your ~/.bashrc to make sure you are setting your PATH properly on login, and check your ~/.bash_profile to make sure it contains the line ". ~/.bashrc" so that your ~/.bashrc gets read each time you open a new terminal window.
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Isaac Schwabacher
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AFNI Message Board
You could resample the datasets to have the same resolution and FOV, but this is usually not a good idea because if you resample the anatomical, it'll lose resolution, while if you resample the EPI it will take up enormous gobs of disk space without making your analysis better. The important thing to note is that, essentially, AFNI is storing where these datasets are in space, independent o
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Isaac Schwabacher
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AFNI Message Board
Hi gurus,
I'm playing around with an idea for more slice-aware motion correction and wonder if there is a way to apply a weight to the source dataset as well as the base in 3dvolreg or 3dAllineate.
The idea is to compute the motion parameters for a given slice by shifting some slices in the source one TR such that each time point represented among the slices in a given volume is closer
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Isaac Schwabacher
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AFNI Message Board
Just a note: if you do just want the binaries moved into ~/abin, you can use the INSTALLDIR makefile variable:
make INSTALLDIR=/home/$USER/abin <target>
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Isaac Schwabacher
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AFNI Message Board
It seems like this test might not be valid when there is true activation for both conditions, and the activation regions are close to each other without overlapping. Then we should find activation no more than p_thr of the time, but it might be the case that we are likely to find it more often than that as the clusters bleed into one another. I haven't done the math on this, but it seems l
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Isaac Schwabacher
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AFNI Message Board
On a related note, is there a general way to extract the warps (linear and non-) that were used to make a dataset from its header? I just noticed the (as yet undocumented) ALLINEATE_MATVEC_* attributes while I was writing a script that could make good use of this information if there were an easy way to access it.
Some use cases for this:
- compute total path length traveled by a voxel durin
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Isaac Schwabacher
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AFNI Message Board
If your threshold is set too high, or if you're using one of the discrete colorbars, those values in the mask might be below threshold or map to a transparent color.
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Isaac Schwabacher
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AFNI Message Board
If you look at 3dcalc -help, you'll find this:
The following 27 functions are used for statistical conversions,
as in the program 'cdf':
fico_t2p(t,a,b,c), fico_p2t(p,a,b,c), fico_t2z(t,a,b,c),
fitt_t2p(t,a) , fitt_p2t(p,a) , fitt_t2z(t,a) ,
fift_t2p(t,a,b) , fift_p2t(p,a,b) , fift_t2z(t,a,b) ,
fizt_t2p(t) , fizt_p2t(p) , fizt_t2z(t)
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Isaac Schwabacher
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AFNI Message Board
Hi Emperor Zhark,
Thank you again for implementing the statistic-as-alpha feature (and so quickly!). It has already become my default view for browsing functional datasets, and I was thinking, in the immortal words of Tom Lehrer, "More, more, I'm still not satisfied!" I mean... um, it would be really awesome if I could use the Clusterize plugin with AFNI_FUNC_ALPHA turned on.
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Isaac Schwabacher
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AFNI Message Board
Pipes are implemented with a buffer, so writing to a pipe writes to the buffer immediately if there's space but waits for space to open up if there isn't. Likewise, reading from a pipe reads from the buffer if there's anything in it, but waits for something to be there if there isn't. When the reader has read enough and closes the pipe, a subsequent attempt to write to the b
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Isaac Schwabacher
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AFNI Message Board
SIGPIPE usually isn't an error, it's just something that happens when you pipe to a program that doesn't read its entire input (which is why plain grep doesn't do it, but grep -m1 does). I'm not sure why AFNI complains about it so loudly.
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Isaac Schwabacher
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AFNI Message Board
You could use a sub-range selector: 3dBrickStat -slow -max fred+orig"<0..$limit>"
(Without -slow, AFNI will out-clever itself and you'll get your limit back unless it's greater than the original dataset's max value)
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Isaac Schwabacher
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AFNI Message Board
No problem! It sounds like you had a lot less trouble building with clang on Yosemite than I did with gcc!
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Isaac Schwabacher
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AFNI Message Board
Clang uses C99 inline semantics, which means these functions need to be declared static. Try this patch:
diff --git a/afni_src/mri_warp.c b/afni_src/mri_warp.c
index 2bc65d8..ef37ac5 100644
--- a/afni_src/mri_warp.c
+++ b/afni_src/mri_warp.c
@@ -23,7 +23,7 @@
static float sx_scale , sy_scale ; /* global scaler data */
-INLINE void xxMRI_scaler( float xpr, float ypr, float *xx , fl
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Isaac Schwabacher
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AFNI Message Board
I was going to fix it quickly in THD_write_datablock, but there are way too many code paths into that function with write_brick set to false for me to be comfortable doing that without a lot of testing. I don't want to fix 3dcopy only to break 3dUndump.
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Isaac Schwabacher
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AFNI Message Board
It looks like 3dcopy reads the .HEAD file into a header struct, changes the ID and writes it back out, but just copies the .BRIK file. Presumably the new header is incorporating the setting of AFNI_BYTEORDER, but this change isn't getting incorporated into the new .BRIK file. THD_write_datablock contains this comment:
/*---------------------------------------------------------------------
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Isaac Schwabacher
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AFNI Message Board
I ask a stupid question, I get an obvious answer. >.<
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Isaac Schwabacher
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AFNI Message Board
Out of curiosity, how are you planning to deal with the movement from swallowing?
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Isaac Schwabacher
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AFNI Message Board
Setting AFNI_NOREALPATH=YES might work; the description in README.environment suggests that the canonicalization is only applied for cosmetic purposes, but the canonicalized version might be getting used somewhere else.
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Isaac Schwabacher
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AFNI Message Board
It seems like this confusion could be reduced somewhat if warp datasets and .aff12.1D files had notes or comments naming datasets in the domain and target spaces, respectively:$ cat T1High_ns_at.nii.Xaff12.1D
# 3dWarpDrive matrices (DICOM-to-DICOM, row-by-row):
# From: T1High_ns.nii.gz
# To: T1High_ns_at.nii.gz
0.975364 0.0454151 -0.00810694 -1.49083 -0.0376654 0.95641
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Isaac Schwabacher
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AFNI Message Board
This might work, but I don't have a good enough model of how quoting works in tcsh to be sure this is robust. Try replacing your sed invocation with this: "1D: `sed -n $start_index,$end_index'H;"\$"{;g;s/^\n//;s/\n/ \\ /g;p;}' ./Onset_Sub$subj/cond4/Event1_times_sub_$subj.txt`"
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Isaac Schwabacher
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AFNI Message Board
I still don't know what's causing your problem, but here's something you can try:
- at the command line, type nano ~/.cshrc
- in the editor, type set path = ( $path $HOME/abin/macosx_10.7_Intel_64 )
setenv DYLD_FALLBACK_LIBRARY_PATH $HOME/abin/macosx_10.7_Intel_64 (or copy-paste from this forum)
- type CTRL-O to save
- hit ENTER to accept the file name listed near the bottom
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Isaac Schwabacher
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AFNI Message Board
I see one issue with this, but fixing it isn't going to be enough to make things work: since your afni programs aren't directly in $HOME/abin but in $HOME/abin/macosx_10.7_Intel_64, you need to use that directory instead of $HOME/abin. But that's not the cause of the errors you're seeing, which baffle me.
The only thing I can think of is that you might have copied the comm
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Isaac Schwabacher
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AFNI Message Board