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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 Daniel,
Thanks for your help. I am digging this data back up now and never really worked through this problem.
I tried your fix and it's almost there but I think that the real problem is the phase-encoding direction needs to be switched. I've used the help page from 3dQwarp to get me slightly further, I think.
##I used Dimon to bring all of the DICOM files into one functi
by
Andrew_Lynn
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AFNI Message Board
Hi All!
Can anyone verify that the spec matrix in my previous post has the appropriate number of free and fixed parameter? I still can't get my model to run but don't see where I've specified something incorrectly.
Best,
Andrew
by
Andrew_Lynn
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AFNI Message Board
Hi Gang,
I'm getting the same error as Pheobe above using this matrix:
L_MT L_V4color L_fef L_ip L_it L_lpfc L_v1 R_MT R_V4color R_fef R_ip R_it R_lpfc R_v1
L_MT 0 0 NA NA 0 NA 0 NA 0 NA NA 0 NA 0
L_V4color 0 0 0 0 NA NA 0 0 NA 0 0 NA NA 0
L_fef 0 0 0 0 0 NA 0 0 0 NA 0 0 NA 0
L_ip 0 0 NA 0 0 NA 0 0 0 NA NA 0 NA 0
L_it 0 0 0 0 0 NA 0 0 0 0 0 NA NA 0
L_lpfc 0 0 0 0 0 0 0 0 0 0 0 0
by
Andrew_Lynn
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AFNI Message Board
JK
I wasn't able to find a work around in batch. I just hardcoded my selections for each question that pops up in the interactive mode and saved it as a new 1dSVAR script. I'm not very experienced using batch and R so this was (more time consuming) easier for me to work around.
Andrew
by
Andrew_Lynn
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AFNI Message Board
Hi Gang,
Yes, I tried to provide and answer to that question. When I used the syntax you've suggested it doesn't seem to get past the first specification. The text file with the command lines is as follows:
source("~/abin/1dSVAR.R")
1
14
1
P0172_svd_mat.1D
0
L_MT
L_V4color
L_fef
L_ip
L_it
L_lpfc
L_v1
R_MT
R_V4color
R_fef
R_ip
R_it
R_lp
by
Andrew_Lynn
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AFNI Message Board
in this myCMDs.R file, should each command be a new line? and should all the subjects be concatenated into one file?
When I use the syntax you've specified, this is the error I get:
[1] "Use CNTL-C on Unix or ESC on GUI version of R to stop at any moment."
Analysis type (0: quit; 1: individual; 2: group)?
Error in if (anaType == 1) { : missing value where TRUE/FALSE nee
by
Andrew_Lynn
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AFNI Message Board
Hi Everyone,
I am trying to run 1dSVAR on an individual subj level and can't seem to get the model to work..am I specifying something incorrectly in the spec matrix?
This is the error I get:
Error in SVAR(x = fm, estmethod = "direct", Amat = instMat, Bmat = bb, :
Model is not identified,
choose different settings for 'Amat' and/or 'Bmat'.
by
Andrew_Lynn
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AFNI Message Board
I need to dicom to nii a set of data where the phase encoding switched A-P to P-A each TR. Is there a switch in Dimon that I am missing? to in to3d?
by
Andrew_Lynn
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AFNI Message Board
here is the command and output.. (it also missed about half of the file)
Dimon -infile_pattern "*dcm" -GERT_Reco -gert_create_dataset -dicom_org -sort_by_acq_time -gert_write_as_nifti -gert_to3d_prefix ${subID}_rest
Dimon version 4.11 (March 13, 2015) running, use <ctrl-c> to quit...
-- scanning for first volume
-- reading 4522 image files ... 100%
-- first
by
Andrew_Lynn
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AFNI Message Board
Hi Rick,
Just as an update, I noticed that there was a file called "upload.dcm" that was not included in the image pattern call...so I changed the code to this
Dimon -infile_pattern "*dcm" \
-gert_create_dataset \
-dicom_org \
-sort_by_acq_time \
-gert_write_as_nifti \
-gert_to3d_prefix ${subID}_rest
but now it looks like each step in the time series i
by
Andrew_Lynn
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AFNI Message Board
Hello,
I am attempting to convert dicoms into nifti files. The data I have are from a data consortium with multiple scan sites and thus it's not easy for me to trouble shoot how the dicoms are ordered/named.
subID=Pxxxx
Dimon -infile_pattern "${subID}*dcm" -gert_create_dataset -dicom_org -sort_by_acq_time -gert_write_as_nifti -gert_to3d_prefix ${subID}_rest -use_l
by
Andrew_Lynn
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AFNI Message Board