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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
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Sorry for the delay. Was away for a bit, but here is the output for that command.
#Magnitude Freq Cum_Freq
0 111854 111854
207 12482 124336
413 6246 130582
619 3770 134352
825 2390 136742
1032 1800 138542
1238
by
tamiskovich
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AFNI Message Board
Hello AFNI experts,
I am getting an error when I try and use the MNI152 template. Here is my proc.py script but for some reason it won't register the template. Pathways are all correct, permissions are fine and proc.py does not crash, just says it will use the default.
**failed to find tlrc_base 'MNI152_T1_1mm.nii
afni_proc.py \
-subj_id ${subject} \
-script ${singlesubscript
by
tamiskovich
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AFNI Message Board
Hello AFNI experts,
I cannot figure out why my proc.py script is failing at automask. Here is the script and error
afni_proc.py \
-subj_id ${subject} \
-script ${singlesubscripts}/proc_${subject}.stop_Qwarp_b4 \
-scr_overwrite \
-out_dir ${subfolder}/${subject}/stop_results_Qwarp_b4 \
-dsets ${subfolder}/${subject}/${subject}.iStar.Stop1+orig ${subfolder}/${subject}/${subject}.iStar.St
by
tamiskovich
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AFNI Message Board
Yes sorry, that is a short rest. The actual stimulus is 1 sec and the ITI from what I see varies from 3, 4, or 5 seconds, the differences in the timing files are 4,5, or 6, from what I am counting.
by
tamiskovich
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AFNI Message Board
Yes, that is the case that they are basically split in half for the primary design. Here are the stim times for the first run as well as the nodata script adjusted for the 1 run. Thank you for the help!
3dDeconvolve \
-nodata 206 2 \
-polort 3 \
-num_stimts 2 \
-stim_times 1 congruent.1D 'GAM' \
-stim_label 1 congruent \
-stim_times 2 incongruent.1D 'GAM' \
-stim_lab
by
tamiskovich
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AFNI Message Board
Hello Afni experts,
I have a question about my design that I ran through 3Ddeconvolve with the no data option.
I want to run a secondary analysis just looking at congruent and incongruent trials for the task. When I run the timing through the no data option it notes very good for each matrix, but when i run 1d_tool.py to look at the correlations it says the correlation between congruent and
by
tamiskovich
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AFNI Message Board
Hi Ziad,
I wanted to follow up on this with you, because I am getting some weird results on the mask.
I did as we discussed and ran the MNI152 through the freesurfer pipeline and mapped the ROI off of that surface to the volume. Attached is the volume ROI on the MNI152 volume on the left and the orginal surface mask from SUMA on the right, and below is the 3dSurf2Vol script. Things look a l
by
tamiskovich
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AFNI Message Board
Hi Ziad,
You helped me greatly with this at the 2014 bootcamp, and I was able to use the mask for surface based analyses. Now I am trying to convert the mask to the volume and I have a few questions about this.
First, how would it be best to get this into a normalized space (i.e. MNI). Should I map it using the MNI spec files to the MNI volume, or could I 3dSurf2Vol it on a subject then war
by
tamiskovich
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AFNI Message Board
Hello AFNI experts,
I am running single subjects through proc.py with the surface options added (script added below)
most subjects are running through okay, but I am getting this error with a couple of subjects.
Error: SkullStripping failed.
Failed.
** ERROR: failed to open -sv dataset, sub273_SurfVol_Alnd_Exp+orig
** ERROR: failed to open -sv dataset, sub273_SurfVol_Alnd_Exp+orig
by
tamiskovich
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AFNI Message Board
Hi all,
I'm looking for some help in using my significant group cluster from FreeSurfer as a mask in SUMA/AFNI.
First, I am curious if I would use @SUMA_Make_Spec_FS or FSread_annot to do this. Second, does it make sense to map the group label to each individual in FS and then transfer to AFNI or keep it on the FSAverage brain then transfer it.
I appreciate any help with this!
Ta
by
tamiskovich
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AFNI Message Board
Hi All,
I could still use some help on this issue.
I am wondering whether @SUMA_Make_Spec_FS or FSread_annot are the programs I need and if so I have a few questions in regard to editing them.
Thanks!
Tara
by
tamiskovich
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AFNI Message Board
Yes it does.
Should I just put the label in the fsaverage folder and run the script on them?
If I want to use this as an fmri mask should I convert the label to volume prior to @SUMA_Make_Spec_FS?
Sorry I'm pretty new to this!
Thanks,
Tara
by
tamiskovich
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AFNI Message Board
Hello Afni experts,
I am trying to move a group surface label created in freesurfer (on the fsaverage) into AFNI space, in order to use as a seed region for a connectivity analysis.
I am a little bit new to this and could use some guidance about the best way to go about this.
I understand I will be using @SUMA_Make_Spec_FS, but I need a little guidance. First I am not sure if I should ma
by
tamiskovich
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AFNI Message Board