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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 Rick
Thanks for your answer.
Sorry for being late to write.
Actually I don't know if I'm using non-linear registration...
I'm just using "@auto_tlrc -base MNI_caez_N27+tlrc" (or with MNI152_T1_2009c+tlrc)...
But you're rigth I can try to run the recon-all of Freesurfer on the MNI152_T1_2009c+tlrc to see if I can have the surfaces...
thus with both temp
by
Alain Guillaume
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AFNI Message Board
Hi Rick,
Thanks a lot for this quick answer.
I would then just have a follow up question :
Let's say I align all my individuals stats with MNI152_T1_2009c+tlrc
Then I'm doing a t-test on that.
Would it be possible to visualize/project the result on the MNI FreeSurfer data that you distribute on your website (because if I understand well it is surface data from MNI_caez_N27 not
by
Alain Guillaume
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AFNI Message Board
Dear afni people,
I'm trying to be sure of my analyses from the beginning :
What is the best template to align everything (anat of subjects and EPI) to MNI space with afni ?
Could I use "MNI_caez_N27" ? (an by the way what is the difference with "MNIa_caez_N27" ?
I would like after that to use the FreeSurfer brain surfaces in MNI space (Based on the anatomical
by
Alain Guillaume
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AFNI Message Board
Hi Daniel,
Sorry I took a long time before being back to you.
Thanks a lot for your advice. I was indeed able to follow the examples 5a and 5b of the afni_proc.py. I have now a script that works fine and everything seems to be well taken into account.
I used RetroTS.m.
But I'm remaining with my first question :
To use RetroTS.m we have first to chop off unneccessary values in phys
by
Alain Guillaume
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AFNI Message Board
Dear Afni People,
I had a crash with a script generated by afni_proc.py, at the step of the blurring...
I'm sending the .afni.crashlog (I tried several times, always the same crash)
What is strange is that this script ran perfectly well for several subjects before crashing with this one.
Do you have any idea of why we have this crash?
Thanks a lot for your attention and your help.
Al
by
Alain Guillaume
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AFNI Message Board
Hi,
Thanks for the reply.
If I use RetroTS.m :
I'm doing :
Opt.Respfile = 'physio_resp_r1.1D' %my raw resp file
Opt.Cardfile = 'physio_card_r1.1D' %my raw puls file
Opt.VolTR = 2.0
Opt.Nslices = 37
Opt.PhysFS = 50
Opt.SliceOrder = 'alt+z'
RetroTS(Opt)
So I'm using here raw physio files as input. I just chopped them to have the correct lengt
by
Alain Guillaume
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AFNI Message Board
Dear Afni People,
I'm trying to correct for physiological noise (card and resp) with 3dretroicor.
Data were acquired with a Siemens 3 Tesla whole-body MRI and I have the ".puls" and ".resp" (50Hz for both) files for all the runs.
In these file I have the raw physio recordings + LogStartMDHTime and LogStartMPCUTime (among differents other parameters).
And on the ot
by
Alain Guillaume
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AFNI Message Board
Thanks for your answers Rick and Ziad,
Concerning the update, unfortunately i cannot do that right now: the afni ver I use is on a network of computers and I need the administrator help to do that and he is not available for the moment.
Nevertheless, it seems indeed that the problems I'm facing are due to some bugs that could be solved by an update: I understood that things go wrong in
by
Alain Guillaume
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AFNI Message Board
Hello,
I'm trying to understand why things go wrong (see my previous posts).
I was again trying to compare activations obtained in the surface space to those obtained in the volume space (same data, same GLM analysis but done separately) and I had crash of suma
Here the commands I used :
afni -niml &
underlay NS20_SurfVol_Alnd_Exp+orig (NS20 being my subject id)
then I sta
by
Alain Guillaume
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AFNI Message Board
Thanks for your quick answer
afni -ver:
Version AFNI_2011_12_21_1014
[]
Yes I used "-oob_value 0"
In fact I followed the Afni_tuto_data6 (with the subject FT) apart that I added the standarization of the surfaces.
Why I see that ther is some mis-registration:
1: the task of the subjects was just to make saccade. So I know that there is some visual activity and broadly in th
by
Alain Guillaume
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AFNI Message Board
Hello,
I have a problem with suma.
Maybe coming from an error on my part.
(I tried to find information on the forum but without success)
I made a group analysis with suma.
For each subjects I used:
@SUMA_AlignToExperiment
and
3dVol2Surf with standard surfaces (std.141.${subj}_${hemi}.spec)
and then I made a ttest with respect to zero with 3dttest++ using all my *.niml.dset file
by
Alain Guillaume
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AFNI Message Board
Thanks for your answer Rick.
And... Oops : I understand my mistake.
The two templates are indeed different.
This is the same data (avg152), but putted in the two different spaces (Tal and MNI).
Sorry for this beginner mistake (which I am)!
Alain
by
Alain Guillaume
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AFNI Message Board
Dear Afni People,
I have a simple question (I tried to search for the answer but was not able to find something)
In my Afni directory, I have the templates: TT_avg152T1+tlrc and MNI_avg152T1+tlrc.
is there some differences between these two templates?
they seem to be exactly identical...
is TT_avg152T1 only the afni way of naming MNI_avg152T1?
Thanks by advance
Alain
by
Alain Guillaume
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AFNI Message Board