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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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Pages: 12
Results 1 - 30 of 37
Dear AFNI experts,
I am writing to ask your opinion and suggestions about longitudinal resting-state analyses.
In the literature I found several studies that just analyzed resting-state data acquired at different time points as independent data, and then "took care" of the longitudinal nature of the analysis only at the group analysis stage.
I would like your opinion about that, si
by
gbattist
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AFNI Message Board
Dear all,
thank you for your message. Actually, I had been told that the PC had the new version of AFNI but I did not realize that the .bashrc was still pointing to the old version; my bad..
thanks
giovanni
by
gbattist
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AFNI Message Board
Dear expert,
I am running @SSWarper on a new machine to get the transformation from the T1 subject space to the MNI. Here the command that I am running:
@SSwarper -input T1.nii -base MNI152_2009_template_SSW.nii.gz -subid sub006
I get the following error right after the first pass of skull stripping:
* ERROR: Totally bogus option '-awarp'
Here's hoping these excerpts f
by
gbattist
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AFNI Message Board
thank you very much for your response. i will definitely do that.
Giovanni
by
gbattist
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AFNI Message Board
Dear AFNI experts,
I would like to register some ROIs in the MNI space to the T1-space of one participant.
I used auto_warp.py to to extract the transformation T1-2-MNI space and then use 3dNwarpApply to apply the inverse transformation to my ROIs. While the direct transformation looks fine (t1 to MNI), when I apply the inverse transformation my ROIs are not correctly registered. Could you
by
gbattist
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AFNI Message Board
Dear Daniel and Paul,
thank you very much for your messages. Actually, the command works by putting the -resample option to off. It is an error that I started having since I received the new pc at work....
Thank you Paul for the useful link; it is definitely something useful with DTI data.
Thanks
Giovanni
by
gbattist
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AFNI Message Board
Hi,
I would like to register an epi image (b0 image from a diffusion acquisition) to the MPRAGE scan of the same subject using align_epi+anat.py, but I get the following error:
bash-3.2$ align_epi_anat.py -anat IC004-4_t1_std.nii -epi IC004-4_dti_b2500_SC_EC_t2di.nii.gz -epi_base 0 -suffix T12b0 -deoblique off -tshift off -master_anat IC004-4_dti_b0.nii.gz
#++ align_epi_anat version:
by
gbattist
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AFNI Message Board
Hi Rick,
I tried to run the command with an updated version of AFNI and everything works fine.
Thank you very much for your help.
Best,
Giovanni
by
gbattist
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AFNI Message Board
Thanks for your help Rick. I have sent you an email with the files you requested.
Best,
Giovanni
by
gbattist
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AFNI Message Board
Dear AFNI experts,
I am running stats in AFNI on gyrification index images calculated with Freesurfer. I would like to perform correction for multiple comparisons on the results of the t-test and I am having some problems with slow_surf_clustsim.py to determine the minimum surface size to threshold my results.
The command I am running is
slow_surf_clustsim.py -save_script surf.sim.15_10
by
gbattist
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AFNI Message Board
Dear AFNi experts,
I am running stats in AFNi on gyrification index images calculated with Freesurfer. I would like to perform correction for multiple comparisons on the results of the t-test and I am having some problems with slow_surf_clustsim.py to determine the minimum surface size to threshold my results.
The command I am running is
slow_surf_clustsim.py -save_script surf.sim.15_10it
by
gbattist
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AFNI Message Board
Hi Peter,
thank you very much for your reply. I will try with the other options you suggest.
Best,
Serena
by
gbattist
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AFNI Message Board
Hi,
I have a question concerning the correction for multiple comparisons for VBM data. I have processed my VBM data with the cat 12 toolbox for Matlab, and then run t-tests between my groups of interest in AFNI using 3dttest++. In order to correct for multiple comparisons the results of 3dttest++, I followed the procedure that is now recommended, including getting the data smoothness with 3dF
by
gbattist
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AFNI Message Board
Dear experts,
I have a question regarding the AlphaSim command for FWE correction of fMRI data.
Is there any substantial difference between using AlphaSim and 3dClustSim, apart from the option of having cluster size for multiple p-values in the latter command?
Thanks
Giovanni
by
gbattist
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AFNI Message Board
These are the output of the 3dmaskdump and 3dROIstats, saying the mask and input dataset need to have the same number of nodes:
3dmaskdump -mask L_SPC_SDvsHV.niml.dset -o test_timeseries HV/1_lh.thickness_fsaverage_smooth10.gii
++ 3dmaskdump: AFNI version=AFNI_2011_12_21_1014 (Dec 22 2015) [64-bit]
** FATAL ERROR: Input and mask datasets are not same dimensions!
3dROIstats -mask L_SPC_S
by
gbattist
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AFNI Message Board
Dear AFNI experts,
I want to extract the subjetcts' mean cortical thickness value in specific ROIs. The ROIs are surfaces extracted from a t-test (.niml.dset) and the images are cortical thickness maps converted in GIFTI format.
I tried using using 3dROIstats but it gives me an error since it requires both ROI_mask and input dataset to have the same number of nodes.
To do that, I tri
by
gbattist
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AFNI Message Board
thanks Peter it works perfectly.
I have one last question to ask you.Once all ROIs extracted I want to extract the mean cortical thickness values for each subject in each ROI.
I tried using using 3dROIstats but it gives me an error since it requires both ROI_mask and input dataset to have the same number of nodes.
To do that, I tried both ROIgrow and ConvertDset to mask the subject cortica
by
gbattist
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AFNI Message Board
thanks Peter, that should work in my case too.
I was now trying to extract an ROI mask dataset on the significant clusters of my group analysis (3dttest++).
I'm trying to use SurfClust -out_roidset to do that but I get the following error:
SurfClust -surf_A lh.SD_vs_HV_ageGenderCov.gii'[1]' -athresh 2.66 -out_roidset -prefix test
where lh.SD_vs_HV_ageGenderCov.gii'[1
by
gbattist
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AFNI Message Board
Thanks for your help Peter.
I used already blurred files in Freesurfer, so I need to estimate the final smoothness of the data. Does anyone know how to do that on surface files?
-giovanni
by
gbattist
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AFNI Message Board
Dear Peter,
thanks for your help.
I was wondering if I could get some help with the parameters for slow_surf_clustsim.py
This is the example provided in the help of the command:
slow_surf_clustsim.py -save_script surf.sim.3 \
-on_surface yes \
-uvar blur 3.0 \
-uvar spec_file sb23_lh_141_std.spec
by
gbattist
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AFNI Message Board
Dear AFNI experts,
I used Freesurfer to extract cortical thickness maps from MPRAGE images. Then, I converted those maps in GIFTI format so AFNI could read those files, and I preformed t-test and ANOVA in AFNI. Now, I would like to correct those results for multiple comparisons. Is there a tool in AFNI, similar to Alphasim, to perform the correction on surfaces?
thanks for your help
giovanni
by
gbattist
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AFNI Message Board
Hi,
I'm running a TBSS analysis on diffusion data to compare fractional anisotropy (FA) between patients and controls. I would like to run the group statistics in AFNI and correct for multiple comparisons using Alphasim.
Given the nature of the "skeletonized" FA , does it make sense to use AlphaSim?
thanks,
giovanni
by
gbattist
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AFNI Message Board
Hi!
I still have a question. I estimated the smoothing kernel size based on the residuals as you suggested me.
Then, in 3dClustSim I restricted the simulation on the gray matter by creating a binary mask of the GM in the original voxel size of the resting-state acquisition (3.75x3.75x4) and not using the voxel-size of the Z and residuals maps (2x2x2 mm in talairach space).
I got a cluster
by
gbattist
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AFNI Message Board
thanks very much Gang.
Just one additional clarification. My images are on Talairach space (res 2x2x2 mm). Do I have to resample the residuals time-curse of each subject to the original voxel size of the resting state acquisition (3x3x3.5)?
giovanni
by
gbattist
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AFNI Message Board
Hi!!
I analyzed resting-state data using the melodic ICA / dual regression toolbox and now I wanna run group statistics using afni and AlphSim for multiple comparison correction.
The output of the dual regression is a Z-score map that quantify, within each subject, each voxel's connectivity with each network identified with the group ICA, plus a residuals time-course image . The Z map is t
by
gbattist
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AFNI Message Board
Hi guys,
I have a question regarding group statistics with unbalanced number of subjects in each group.
I need to run an ANOVA with factor GROUP (HV, PatientGroup1, PatientGroup2, PatientGroup3) and TASK (Speech, syllable1, syllable2).
The problem is that I cannot run 3dANOVA3 because of unbalanced number of subjects in each group (27 HV, 27 PatientGroup1, 26 PatientGroup2, 20 PatientGroup
by
gbattist
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AFNI Message Board
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