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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 4 of 5
Pages: 12345
Results 91 - 120 of 128
rick reynolds Wrote:
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> Look at your pb0* datasets, scaling is the last
> preprocessing step. Please review the proc
> script so that you know what commands are
> being executed.
Thanks! So according to the script, it appears to me that pb04* should be the dataset after blurring (pb03) and scaling?
Sorry, but I am a s
by
maitra
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AFNI Message Board
Thanks, Rick! What is the scaling that should happen here?
Also, I do not seem to have @ss_review_driver in my list of commands. Do I have to install it from somewhere? I am using the linux_xorg7_64 binary build provided by AFNI.
Many thanks again!
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hi,
I used uber_subject.py to do my (single subject) analysis and got a bunch of files. I understand at least some of them, but I was wondering if there is a way to access the registered/aligned EPI volumes.
Here are all the files I got:
3dClustSim.cmd* mat.r01.vr.aff12.1D*
all_runs.Imag_anat2epi.nii.gz* mat.r01.warp.aff12.1D*
all_runs.Imag_anat2epi+tlrc.BR
by
maitra
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AFNI Message Board
Thanks! Sorry, this got buried and I did not see this response. I am going through Freesurfer right now as per the tutorial.
Btw, I was wondering: is the aligned functional volume stored anywhere in the output of uber_subject.py? I was assuming that this was in the all_runs.Imag_anat2epi+tlrc. files but this seems to be something else (the images are too noisy and do not appear to have any def
by
maitra
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AFNI Message Board
Hi,
I am very new to AFNI and even newer to SUMA. I am trying to learn the ropes with a basic analysis on a single-subject tennis-playing imagination experiment.
I have an original anatomical dataset is: 110 x 208 x 202, and a functional EPI dataset of dimension 64x64x30 over 105 time-frames with different FOVs (as specified in the file headers).
I believe that I have, with generous ass
by
maitra
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AFNI Message Board
Gang Wrote:
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> > Gang: can I use a dataset as covariate in
> 3dttest++?
>
> Yes. Read the 3dttest++ help for the usage and
> details.
>
> I don't know the context of your analysis.
> However, it's generally not considered a good idea
> to perform analysis on statistics including
> t-sta
by
maitra
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AFNI Message Board
claudio_gentili Wrote:
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> Hi, thanks for your answers:
> Gang: can I use a dataset as covariate in
> 3dttest++?
> Ranjan: would I have to transform my dataset in R
> matrix than.
No, all you would have to do is to read it in. You can use read.AFNI from the package 'fmri' and then use extract.data() to obtain
by
maitra
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AFNI Message Board
This is an interesting question that you have raised. I am assuming that you have the t-statstics for the two conditions at each voxel which is what I would use (rather than the beta coefficients which are not standardized by their standard deviations). I would simply calculate the correlation using the cor() function in R and report it.
Ranjan
by
maitra
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AFNI Message Board
I guess, my question is given the aligned functional image and the aligned anatomic image, how do I get the two image volumes aligned. My confusion stems from the fact that both these appear to be aligned to different coordinate systems.
Btw, here is the script that uber_subject.py threw out:
#!/usr/bin/env tcsh
# created by uber_subject.py: version 0.36 (April 5, 2013)
# creation dat
by
maitra
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AFNI Message Board
Gang Wrote:
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> OK, I didn't notice the following sentence of
> yours:
>
> > Is there a way to get the one-sided upper tail
> p-value?
>
> Then do this:
>
> 3dcalc -a stats.Imagination001_REML+orig'[4]'
> -expr
> 'ispositive(-a)*(1-fitt_t2p(a,20)/2)+ispositive(a)
> *fi
by
maitra
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AFNI Message Board
Hi Gang,
Thanks!
> 3dcalc -a stats.Imagination001_REML+orig'[4]'
> -expr 'fitt_t2p(a,27)/2' -datum float -prefix
> brick4p_one_sided
This will not do it. I guess it has to be something like:
if the t-statistic is negative, then the value is 1 - fitt_t2p(a,27)/2 and if the t-statistic is nonnegative, then it is fitt_t2p(a,27)/2.
So, I think it should
by
maitra
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AFNI Message Board
Hello again!
So, looking at the example in the cdf -help, I get:
ccalc -expr 'fitt_t2p(3,20)'
0.007076
which appears to be the two-sided p-value.
Is there a way to get the one-sided upper tail p-value?
Otherwise, I guess we need to write a function which assigns 1-half the current value if the t statistic is negative, and half the current value if the t-statistic is posi
by
maitra
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AFNI Message Board
Thanks very much again, Rick!
Here is where I am lost.
The original anatomical dataset is: 110 x 208 x 202, the functional is 64x64x30, with different FOVs (as specified in the file headers).
However, the datasets that come out in the functional (epi) after alignment and processing are: 46 x 55 x 43. The anatomic is: 161 191 151. So I am confused as to where the aligned anatomic image
by
maitra
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AFNI Message Board
Hi,
I tried having the alignment done by afni_proc.py (with script created by uber_subject.py) and got results. I presume that here the result is that the anatomic image volume is aligned to the time-registered functional volume image by default. Fine, but where is the anatomic image aligned to the functional image stored?
Many thanks,
Ranjan
by
maitra
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AFNI Message Board
Dear Emperor Zhark,
Thank you very much!! This sort of help is really very useful for me! And you are right, I am indeed a new user!
Many thanks again!
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Thanks, Gang!
I am wanting to use the p-values for further computations and improved activation detection. I have a single subject single experiment (imagination dataset of healthy volunteer imaging playing tennis) . I ran 3dREMLfit and got the following files:
stats.Imagination001+orig.BRIK
stats.Imagination001_REML+orig.BRIK
Which of these would have the test statistics (would it be
by
maitra
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AFNI Message Board
Hi,
I ran 3dREMLfit using the proc_afni.py script:
3dREMLfit -matrix X.xmat.1D -input pb04.Imagination001.r01.scale+orig.HEAD \
-fout -tout -Rbuck stats.Imagination001_REML -Rvar stats.Imagination001_REMLvar \
-Rfitts fitts.Imagination001_REML -Rerrts errts.Imagination001_REML -verb $*
Now, I want to get the p-value for the test statistic for detecting activation at each voxel for
by
maitra
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AFNI Message Board
Hi,
I have been trying to learn to use AFNI. I have previously, with the generous help of this list, been able to align my functional to my anatomic dataset (using align_epi_anat.py). So, on to the next step of the analysis: I have noticed that the afni_proc.py itself has an alignment option (and by default this is created by the script uber_subject.py).
Is using the afni_proc.py on the unal
by
maitra
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AFNI Message Board
Hi,
I was wondering if it is possible to save the output of align_epi_anat.py in NIfTI format? I tried putting -prefix Imagination_anat_al.nii.gz (as I thought I read somewhere online) but I get:
#++ align_epi_anat version: 1.50
** error: unknown trailing arguments : ['-prefix', 'Imagination_anat_al.nii.gz']
** ERROR - script failed
So, this is clearly not right. An
by
maitra
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AFNI Message Board
Hi,
Aha! I understand this now:
> The timing file that you shoud pass
> to afni_proc.py should look like "30 90 150",
> with basis function 'BLOCK(30)'. That is to say
> there were 3 non-rest events, each lasting 30 s.
The 30 90 and 150 are when the non-rest events started. However, I am still wondering where do I put the fact that there was a time of
by
maitra
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AFNI Message Board
May I also ask, if supplying BLOCK() means that the script will take in and make the HRF? Should the TR be passed on later, by modifying the script that is returned and submitted, as an argument to -force_TR to 3dDeconvolve?
(Just to reiterate for the sake of clarity, I have a TR of 2s, and a total number of 105 time series scans.)
But if I want to use correlated autoregressive errors, s
by
maitra
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AFNI Message Board
Hi,
I have the following task (imagination experiment): Task and rest blocks had a duration of 30 s and were played out in the following order: rest, task, rest, task, rest, task, rest, totaling 105 repetitions. There were 2s between each scan.
From what I understand i should use @make_stim_file.
@make_stim_file -outfile imagination_out
headers -> imag
'imag' -> 16
by
maitra
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AFNI Message Board
Thank you again! Btw, is it possible to write only some slices in the z-plane (say, 56-175, there are 202 in all) and not store the whole thing?
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Daniel Glen Wrote:
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> I haven't tried this, but it might be that it's
> NIFTI format. It's worth trying with AFNI format.
> Use 3dcopy to AFNI format first and repeat with
> the AFNI format equivalent datasets.
Yes, this makes it work, funny that it does not recognize the NIFTI for the -master_anat option. A
by
maitra
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AFNI Message Board
Thanks! This did not get the error out.
Anyway, but I was also trying to register the anatomic with the functional using the following
align_epi_anat.py -anat ../MPRAGEco.nii.gz -epi_base 0 -epi ../Imagination.nii.gz -master_anat ../Imagination.nii.gz -ginormous_move -align_centers yes -save_vr
but I get an error in 3dAllineate. Is it because the functional dataset is a 4-volume datas
by
maitra
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AFNI Message Board
Thanks! Here is what I get:
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.19.1-201.fc21.x86_64
version: #1 SMP Wed Mar 18 04:29:24 UTC 2015
distribution: Fedora 21 Twenty One
number of CPUs: 8
apparent login shel
by
maitra
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AFNI Message Board
Peter,
Thanks very much! The -bigmove is really what I needed to get it going. Btw, it did report an error while doing all this:
...
#Script is running (command trimmed):
3dNotes -h "align_epi_anat.py -anat ../MPRAGEco.nii.gz -epi_base 0 -epi \
../Imagination.nii.gz -epi2anat -big_move -master_epi ../MPRAGEco.nii.gz" \
./Imagination_al
Error: Cannot open dataset
by
maitra
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AFNI Message Board
rick reynolds Wrote:
> If you want the EPI aligned to the
> anat, consider
> adding -epi2anat, and maybe something like
> -master_epi 3.5
> (note that 3.5 mm is the voxel size that
> afni_proc.py would
> use if you were asking it to write the analysis
> script).
Hi Rick and everybody,
I was wondering where this 3.5 mm comes from (should it be 0.94 since we
by
maitra
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AFNI Message Board
Hi,
I am trying to align the data on an imagination experiment of Tabelow and Polzehl (Journal of Statistical Software, 2011) paper available at:
(The above link contains the dataset.)
The authors in private e-mail have confirmed that the dataset are not registered -- either for motion correction in the functional time course sequence of image volumes or to the anatomical. So, I have
by
maitra
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AFNI Message Board
Page 4 of 5
Pages: 12345