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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
Page 3 of 3
Pages: 123
Results 61 - 81 of 81
Dear all,
I'm want to create a mask with spherical ROIs in the MNI space using 3dcalc with the script below, where the coordinates of the ROI centers are in $ROIfile, e.g. 1,-23,34,15.
since the ROIs do not overlap and the initial ROI_parcels_MNI+tlrc. is all zeros (ie. 0*MNI template to obtain the same grid) and the value of iROI*step() must be an integer, I expected that the values i
by
Cesar Caballero Gaudes
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AFNI Message Board
Thanks Daniel.
This option, as well as 3dWarp -mni2tta -NN work perfect.
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
I would like to convert a list of coordinates in MNI space to coordinates in TLRC space (as I used the TT_N27 template for normalization with 3dQwarp). In particular, the list of coordinates are the ones used in Power et al., Neuron 2011
Is there any tool that can do the conversion automatically? whereami offers this feature, but it also returns extra information that I would need
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Cesar Caballero Gaudes
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AFNI Message Board
Hi Anita,
Let me give you my opinion here, apart from Gang's advice. The magnitude of the signal changes greatly depend on BOLD sensitivity and magnetic field strength. Clearly, we expect larger signal changes at 7T than at 3T, and at 3T than at 1.5T, and so on. Furthermore, the BOLD sensitivity varies across regions depending on the magnitude of the change in transverse relaxation R2* (i
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi all,
we are interested in the implementation of real-time fMRI with AFNI, particularly for image quality control purposes, in our Siemens Trio system (currently running with VB17).
I found very useful slides in
and more detailed info in
I was wondering whether there is specific information about the implementation in the Siemens Trio, or someone has managed to implement i
by
Cesar Caballero Gaudes
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AFNI Message Board
Dear Peter,
Thanks very much for your suggestion.
Indeed, adding a pause of 15 seconds (i.e. sleep 15) before launching the plugout_driver sorted out the problem.
I also added the option of saving the images, and many more... plugout_drive has just saved a hell of time...
thanks,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi all,
I'm trying to do a drive afni script that allows me to quickly review the results of the alignments of preprocessing.
To make things simpler, I copied all datasets I want to review into one folder. Basically, the script needs to switch the underlay and overlay volumes for each subject in the original space and tlrc space, and waits for the user to press ENTER to continue. See be
by
Cesar Caballero Gaudes
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AFNI Message Board
Thanks Daniel,
Your answer is very clear.
Best,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Yes, I tried and it seems to do what I say... but I wanted to be sure...
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Rick,
Yes, it is very reasonable....
What you propose would create as many solutions as seed. Then, one could choose the solution with the minimal within cluster sum of distances, which is saved in the output file -write_dists FILE.info1.1D.
Therefore, I was wondering whether the -rep option actually does this and select the solution with minimum within cluster sum of distanes.
If
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Afniers,
I am trying to align a high resolution anatomical T1 image (0.5mm in-plane, 0.8 slice thickness with sagittal acquisition) to a functional image with align_epi_anat.py.
The skull in the T1 image has been removed with 3dSkullStrip and it has also been corrected for intensity inhomogeneities (with FAST).
My command is
align_epi_anat.py -anat2epi -anat T1Div_brain_uni+orig
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Cesar Caballero Gaudes
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AFNI Message Board
Hi rick,
Thanks for the reply. I've just noticed that the option -r in 3dKmeans could serve for this purpose, i.e. running different iterations of the algorithm and each time with different seeds. Is my understanding correct?
Best,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Afniers,
I would like to run 3dKmeans multiple times with different initializations. For that, should the -seed value be changed for each repetition (e.g. with a rnd number generator)? Is that the way to achieve it?
If so, do you know any command to generate valid seed numbers in AFNI or bash?
Thanks,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi,
If I understood correctly your question, this is still possible and available in the AFNI GUI.
In the graph window, click on FIM. Pick the ideal file .1D, and compute the fim (fico) or fim+ (fbuc) in the same menu.
Hope this helps,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hello,
I am trying to get average ROI timecourses for functional connectivity analysis where the ROIs are based on the volumetric FreeSurfer parcellation aparc.2009s+asec.
To achieve that, I tried the following commands for each subject and ROI:
@FS_roi_label -name ${ROI} -rankmap ${FSdirectory}/${subject}/SUMA/aparc.a2009s+aseg_rank.rankmap.1D > label_info.1D
labelnumber=$(1deval -o
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi again,
Similar to my previous question,
Is it possible to select the N subbricks corresponding to the highest or lowest values in an 1D file?
I know that 1dTsort can be used to sort the values in the 1D file but the column index is lost to the best of my knowlege.
Are there any workaround?
Thanks,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi Rick,
Thanks very much for the quick reply. Sorry for the lack of details.
I want to keep the subbricks of the big numbers, and the .1D are already preprocessed so that they only include positive numbers.
You just responded with the more sensible example.
Thanks,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi,
I would like to do a subbrick selection based on when the values in a 1D file are larger than a given number.
The 1D files are created with 3dmaskave using the -quiet option.
So far, I was not able to get this done with a series of 1deval and 3dTcat commands.
Any suggestions or AFNI-magic trick?
Thanks very much for your help,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi again...
The solution is with 3dBrickStat... see the following posts
Sorry for the interruption and thanks,
Cesar
by
Cesar Caballero Gaudes
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AFNI Message Board
Hi all,
I would like to create a mask that only contains the voxels with the highest X% and lowest Y% values of the input dataset. In other words, creating a mask based on the X and Y percentiles of the input data.
I thought of using 3drank (or 3dmerge with -1rank option), but the help indicates that these options only accept input datasets with integer values. I would like to work with i
by
Cesar Caballero Gaudes
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AFNI Message Board
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Pages: 123