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Hi Gang,
Thank you again for your answer,
For the record, here is the new command:
3dLME -prefix /3dLME_glt.nii.gz \
-jobs 8 -model "gender*age" -qVars "age" -ranEff '~1+age' \
-num_glt 5 \
-gltLabel 1 '05MF' -gltCode 1 'gender : 0.5*M +0.5*F age :' \
-gltLabel 2 '1MF' -gltCode 2 'gender : 1*M -1*F age :' \
-gltL
by
Doughboys
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AFNI Message Board
Hi Gang,
Thank you again for your help!!
As advised, I ran the command:
3dLME -prefix 3dLME_.nii.gz -jobs 8 \
-model "gender*age" \
-qVars "age" \
-ranEff '~1+age' \
-dataTable
Subj age Sexe InputFile
Oliver 1128.0 M /Oliver2019_02_02_ztest.nii.gz \
Oliver 1247.0 M Oliver2019_06_01_ztest.nii.gz \
Oliver 1353.0 M Oliver2019_09_15_ztest.nii.gz \
Oliv
by
Doughboys
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AFNI Message Board
Hi Gang,
Thank for your answer!
The subjects were not measured exactly at the same age but within the same session. The effect of interest is the age and I am looking to observe a correlation with the modification of the connectivity strength. As an example, I previously did an extraction of the ALLF signal with an atlas and then calculated the Repeated measures correlation coefficient within
by
Doughboys
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AFNI Message Board
Hello AFNI experts in statistics,
I would like to measure the effect on age on a longitudinal fMRI resting-state dataset (4 repeated measures at a different age) with covariate such has gender.
I already performed the seed base analysis on each subject and now I want to regress the age on each statistical maps in order to observe the age related variation of the DMN connectivity (with gen
by
Doughboys
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AFNI Message Board
Hi AFNI expert,
I finally found the solution and I will probably be able to be more clear.
Two things were impacting the results of this analysis and fixing it has tremendously improved the quality of the coregistration:
1. Deobliquing the data prior to @afni_proc.py can be dangerous if like in my dataset the EPI and the anatomical images have different FOV orientations.
3drefit
by
Doughboys
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AFNI Message Board
Hi --pt,
So sorry for the confusion,
1. The first group of monkeys (including the image that I send to you) has successfully ended. All the images are well aligned with the template (thank you again!) using the protocol that I describe here:
2. I have a second group of monkey that has been scan with another coil. For almost all these 8 monkeys, the coregistration between the functional
by
Doughboys
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AFNI Message Board
Hi again,
sry I am probably not clear at all and I hope that I am not looking in the wrong direction.
The result from your previous command is:
anat
RAI -61.685852 65.814148 -30.202454 97.297546 7.62584587.125847 anatT1.nii.gz
func
RAI -62.152084 63.847916 -21.139194 104.861847 -6.759480 55.241032 BOLD_restingstate.nii.gz
after tranfo:
RAI -62.152084 63.847916 -21.139194 104.861847 -6.7
by
Doughboys
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AFNI Message Board
Hi --pt,
Thank you, I don't think that it is going to work because in the previous pipeline we already align the center of these two images.
I think that the problem comes from the fact that the two images do not overlay.
Probably, when we apply the transformation parameters, they can't be accurate anymore because the orientation of the two brains is different.
The non-overlay of
by
Doughboys
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AFNI Message Board
Hi --pt,
If we go back to what we have done here:
# --------------------- for obliquity and center of mass of EPI
3dcalc \
-a ${dset_bold} \
-expr 'a' \
-prefix ${dset_bold_deob}
# purge obliquity info, and apply shifts so BOLD dset overlays anat dset well
3drefit \
-deoblique
by
Doughboys
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AFNI Message Board
Hi AFNI expert,
I have 1 anatomical image and 1 functional image that has been acquired with two different FOV orientations.
When I use different viewer (AFNI, MRIcron) the images superposed perfectly because (I don't know where but the orientation of the FOV is saved somewhere)
I have to do some manipulation on the images (obliquity, change the centre etc...) and this orientation is
by
Doughboys
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AFNI Message Board
Hello AFNI,
Thanks to --pt I have now the solution for the coregistration of the functional images in macaques:
I had difficulty with nonlinear warping because large shifts were involved:
"basically, the memory usage can be quite high, because the warp field must cover a box that covers both input and output datasets-- and a large shift means that one would need a large box (memory c
by
Doughboys
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AFNI Message Board
Ok, I find a way to do it but I don't know why...
based on the idea that the transformation from 3dNwarpApply was false...
# apply catenated xform: volreg/epi2anat/tlrc/NLtlrc
# then apply non-linear standard-space warp
3dNwarpApply -master anatT1_deob_warp2std_nsu+tlrc -dxyz 2 \
-source pb01.$subj.r$run.tshift+orig \
by
Doughboys
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AFNI Message Board
Hi ptaylor,
Here is the command after @animal_warper
# afni_proc.py -subj_id Oliver2019_02_02 -script \
# /8_Func_AFNI/Oliver2019_02_02/proc.Oliver2019_02_02 \
# -scr_overwrite -out_dir \
# /8_Func_AFNI/Oliver2019_02_02/Oliver2019_02_02.results \
# -blocks tshift a
by
Doughboys
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AFNI Message Board
Hi ptaylor,
Thank you so much for your help!
+ the original coordinates are a bit odd-- while the anatomical and EPI overlay each other, the (x, y, z) = (0, 0, 0) location is far outside the brain; this can affect some alignment issues.
==> Do you have any idea of what could cause that in the aquisiton protocol?
I applied strictly your protocol, and it has improved the co registration
by
Doughboys
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AFNI Message Board
I think also that sharing this images could be the easiest solution. Thank you so much for your help!
Clément
by
Doughboys
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AFNI Message Board
Thank you again!
With pleasure! will let you know when I will start my work on other species.
The 3drefit on warp2std_nsu.nii.gz did a perfect job, to change the space and it has allow afni_proc to continu.
However, when it arrived to
# apply catenated xform: volreg/epi2anat/tlrc/NLtlrc
# then apply non-linear standard-space warp
3dNwarpApply -master anatT1_warp2std_nsu+
by
Doughboys
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AFNI Message Board
Great thank you so much for that!
So which template do you suggest to use? or is there a way to bypass this issu directly in afni_proc and work with the ORIG space?
Maybe I don't understand afni_proc very well, is it totally necessary to have a template in the tlrc space? because I the futur I would like to work with other species and a home made template. Do you think that it will be poss
by
Doughboys
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AFNI Message Board
Hi again,
I downloaded the template at:
3dinfo NMT_SS.nii.gz
Identifier Code: AFN_ZuEbKDcZ-wbFK6dSTdvAsQ Creation Date: Wed Apr 26 15:47:32 2017
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed}
Storage Mode: NIFTI
Storage Space: 86,035,180 (86 million) bytes
Geometry String: "MATRIX(-0.25,0,0,31.75,0,-0.25,0,50.5,0,0,0.2
by
Doughboys
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AFNI Message Board
Hi again,
I downloaded the template at:
3dinfo NMT_SS.nii.gz
Identifier Code: AFN_ZuEbKDcZ-wbFK6dSTdvAsQ Creation Date: Wed Apr 26 15:47:32 2017
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed}
Storage Mode: NIFTI
Storage Space: 86,035,180 (86 million) bytes
Geometry String: "MATRIX(-0.25,0,0,31.75,0,-0.25,0,50.5,0,0,0.2
by
Doughboys
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AFNI Message Board
Hi again,
I downloaded the template at:
3dinfo NMT_SS.nii.gz
Identifier Code: AFN_ZuEbKDcZ-wbFK6dSTdvAsQ Creation Date: Wed Apr 26 15:47:32 2017
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed}
Storage Mode: NIFTI
Storage Space: 86,035,180 (86 million) bytes
Geometry String: "MATRIX(-0.25,0,0,31.75,0,-0.25,0,50.5,0,0,0.2
by
Doughboys
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AFNI Message Board
Also, I just re-downloaded the template and the space remain ORIG. Also, afni_proc seems to required tlrc so even if the space is NMT it will continu to crash no? or is it just ORIG that cause the problem?
by
Doughboys
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AFNI Message Board
Hi ptaylor,
Thank you so much for that answer I think now the origin of my problem is now obvious:
3dinfo -space -prefix /home/cgarin/Documents/1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz
** AFNI converts NIFTI_datatype=4 (INT16) in file1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to s
by
Doughboys
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AFNI Message Board
Hi Daniel,
Thank you so much for this advice! I tried @animal_warper and it work so much better than my own code!
I also tried to apply the parameters from @animal_warper to afni_proc.py and tlrc_NL_warped_dsets.
The warp2std_nsu.nii.gz is well coregistrated with the template and well skullstriped.
However warp2std_nsu.nii.gz is transformed by 3dcopy in warp2std_nsu+orig.HEAD.
afni_proc.p
by
Doughboys
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AFNI Message Board
Hi-
I split this question to a new thread from here:
because it is a somewhat separate question, and the thread has wandered further afield.
--pt
----------------------------------------------------------------------------------------------------------------------------------------
Hi,
I have exactly the same problem as you for NMT to the anat space.
This command has also worked
by
Doughboys
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AFNI Message Board
Hi rick,
yes, it concern only one slice of the EPI image and one slice of the anatomical image that seems well align but with some difference due to the EPI sequence.
I can send these images to you if you want?
I just repeated the error this week on other animals and it seems to appear always in the last axial slice of the brain on which their is probably not enough similar voxels. However, I
by
Doughboys
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AFNI Message Board
Also, i try to copy the header of the anat on the func (due to the minor differences) to see if it change anything but it doesn't...
Thank you again!
by
Doughboys
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AFNI Message Board
Hi rick,
Thank you so much for your answer.
here is the results of the commands:
3dinfo -extent -prefix BOLD_resting*.nii.gz anatT1_unif*
-65.423553 60.576447 -37.874031 88.125969 75.824852 75.824852 BOLD_restingstate
-65.423553 60.576447 -37.874020 88.125977 75.824852 75.824852 anatT1_unifized
3dBrickStat -slow -min -max BOLD_resting*.nii.gz
0 143.973
3dBrickStat -slow
by
Doughboys
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AFNI Message Board
Hi AFNI experts,
I have a problem with 3dQwarp command in trying to allineate on of the slice of my functional with my anatomical images. I am working with primate and I am using a pipeline called sammba MRI that use afni.
The weird thing is that 3dQwarp command has works very well for all the slices of my primate and all the other primates. I don't really understand the error message.
Th
by
Doughboys
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AFNI Message Board
Hi Paul,
Here is the result
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.4.0-17763-Microsoft
version: #379-Microsoft Wed Mar 06 19:16:00 PST 2019
distribution: Ubuntu 18.04 bionic
number of CPUs: 24
apparent login shell: bash
shell RC file:
by
Doughboys
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AFNI Message Board
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