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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 Paul and Rick,
Thanks a bunch!
I tried to upgrade the R and also followed the steps from Paul, which could get the AFNI and SUMA work better, like 3dMVM fixs now.
But when I run the @SUMA_Make_Spec_FS script again, it still stopped and gave error information like:
+ @SUMA_Make_Spec_FS -fspath /Applications/freesurfer/subjects/CRF_S05_TPL -sid CRF_S05_TPL -NIFTI
++ Running @SUMA_Make_S
by
SarahChang
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AFNI Message Board
Hi there,
Here is the original error information:
+ @SUMA_Make_Spec_FS -fspath /Applications/freesurfer/subjects/CRF_S01_TPL -sid CRF_S01_TPL -NIFTI
++ Running @SUMA_Make_Spec_FS version: 2.2.1
** apparent failure to run mris_convert
mris_convert --help starts with:
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfe
by
SarahChang
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AFNI Message Board
I have a similar problem. It seems that I upgraded to 10.12, which is not right?
Here is the information:
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.6.0
version: Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xn
by
SarahChang
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AFNI Message Board
Hi All,
I'm wonder if there are some approaches that could subdivide cortical layers according to its cortical depth (e.g. depth based on the interface between grey matter and white matter). For example, I have a high-resolution anatomical image and a V2 mask, I'm going to separate V2 into superficial, middle and deep layers. Would it be possible to do this kind of analysis with AFNI
by
SarahChang
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AFNI Message Board
Hi Rick,
I just found this page from google when I tried to downsample my data.
Here is the script I'm writing:
3dcalc -a pb03.$subj.vol.r0$#indexrun.blur+orig"[0..$(2)]" \
-b pb03.$subj.vol.r0$#indexrun.blur+orig"[1..$(2)]" \
-expr '(a+b)/2' \
-prefix pb03b.$subj.vol.r0$#indexrun.downs+orig
However, it a
by
SarahChang
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AFNI Message Board
Sorry, but what's meaning of the extra alignment? do you mean an extra manually alignment if I used the NIFTI option? or just use an extra option for alignment? I checked output generated by @SUMA_AlignToExperiment, there is a misalignment after this step. Should I add something like an extra alignment here?
Thanks,
Sarah
by
SarahChang
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AFNI Message Board
And to double check, I also used 3dAFNItoNIFTI in my code. Is there any update for this function?
I checked the help file and found there is a update today? like 3dAFNItoNIFTI: AFNI version=AFNI_18.0.24 (Mar 6 2018) [64-bit]
So does it mean that I need to rerun everything today?
Thanks,
Sarah
by
SarahChang
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AFNI Message Board
Yes, I rerun this step using @SUMA_Make_Spec_FS -fspath $SUBJECTS_DIR/$templatename -sid $templatename -NIFTI before any further processing steps.
I'm wondering if the file sub01.surf_SurfVol_Alnd_Exp+orig is the right one to check the alignment problem. If yes, it is supposed to be aligned to the template, right?
Thanks,
Sarah
by
SarahChang
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AFNI Message Board
Yes! I updated the AFNI to Feb 26 2018 (Version AFNI_18.0.22) and the problem solved .... Sorry, I should check and update AFNI regularly.
But I do have another question. I used freesurfer to generate all the surface information and then used afni_proc.py as below to do preprocessing.
afni_proc.py -subj_id $subj.surf \
-blocks tshift align volreg surf blur scale \
-copy_anat anat+orig \
by
SarahChang
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AFNI Message Board
I updated the AFNI to Feb 26 2018 (Version AFNI_18.0.22) and the problem solved .... Sorry, I should check and update AFNI regularly.
But I do have another question. I used freesurfer to generate all the surface information and then used afni_proc.py as below to do preprocessing.
afni_proc.py -subj_id $subj.surf \
-blocks tshift align volreg surf blur scal
by
SarahChang
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AFNI Message Board
It's May 21 2017 (Version AFNI_17.1.06).
Is ti too old?
by
SarahChang
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AFNI Message Board
And I just found this from the help file:
cd SUMA
tcsh
foreach ss (*.gii)
ConvertSurface -i $ss -o_gii $ss \
-overwrite -xmat_1D NegXY
end
This method doesn't help.
And I couldn't find any options in @RetinoProc about GIFTI/NIFTI
thanks,
Sarah
by
SarahChang
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AFNI Message Board
Hi Daniel,
Thanks for those information. It's very helpful.
But another question is that I need to run @RetinoProc after generating SUMA folder. The problem is something like lh.smoothwm.asc won't be generated with -NIFTI option. With -NIFTI they are all in .gii format. Should I convert all of the .gii files into .asc using 3dcopy?
Thanks,
Sarah
by
SarahChang
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AFNI Message Board
Hi all,
I found a very odd problem. I tried two different ways to generate the suma folder for surface based analysis.
One is:
@SUMA_Make_Spec_FS -sid $subj -fspath $SUBJECTS_DIR/$subj/
The other one is:
@SUMA_Make_Spec_FS -fspath $SUBJECTS_DIR/$subj/ -sid $subj -NIFTI
So the only difference here is the -NIFTI option.
Then I compared the files with the same name (they are suppose
by
SarahChang
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AFNI Message Board
Hi Daniel,
I tried the method you mentioned, unfortunately, I got another error:
#Script is running (command trimmed):
cat_matvec -ONELINE ./sub04_avg_anat_al_junk_e2a_only_mat.aff12.1D /Volumes/fMRI_Data/AFNI_PROCESSED_DATA/vis_loc/sub04_20170516/xform_test.aff12.1D -I > ./sub04_avg_anat_al_junk_mat.aff12.1D
** FATAL ERROR: File '/Volumes/fMRI_Data/AFNI_PROCESSED_DATA/vis_loc/s
by
SarahChang
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AFNI Message Board
Hi Daniel,
The command I used to generate the matrix is:
3dAllineate -prefix anat_within_aligned -base ${subj}_avg_anat+orig -1Dmatrix_save align_to_avg -source anat+orig
And then I used that matrix in afni_proc.py:
afni_proc.py -subj_id $subj.vol \
-blocks tshift align volreg scale \
-copy_anat ${subj}_avg_anat+orig
by
SarahChang
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AFNI Message Board
Hello,
I got an error information as below:
** FATAL ERROR: -matvec file not a 3x4 matrix!
** Program compile date = May 21 2017
** ERROR: Could not oblique/shift anat to epi data
I checked the matrix using in the code, it is a 3*4 matrix. Well, at least it contains 12 numbers.
Here it is:
# 3dAllineate matrices (DICOM-to-DICOM, row-by-row):
1.00309 -0.0030288 -0.0049038
by
SarahChang
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AFNI Message Board
Thanks Rick~
Yes, that method sounds reasonable, I've got the mask in tlrc space.
But I met another problem, when I tried to do the non-linear 3D warp using auto_warp.py, for warping the T1 image to TT_27 template.
Here is the code I used :
auto_warp.py -base TT_N27+tlrc -input ${subject}_TPL.nii \
-skull_strip_input no
by
SarahChang
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AFNI Message Board
Thank you so much Daniel.
I tried to use @auto_tlrc.py. But I aways got the error info like:
What kind of dataset is this?
-- Error 3dSkullStrip (SUMA_3dSkullStrip.c:2019):
Failed to load/prep volume
Error: Failed to create skull stripped brain
Here is the code I'm using:
@auto_tlrc -base TT_N27+tlrc \
-suffix SphereM \
-input AllSubrg_SphereMask+orig \
by
SarahChang
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AFNI Message Board
Hello,
I'm using the new AFNI and want to transform the anat image from native space to TAL. I saw a video on Youtube using a define marker menu to do the transformation. But I can't find it in the new version of AFNI. Can someone help me with that?
Many thanks,
Sarah
by
SarahChang
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AFNI Message Board
Hi all,
I have a problem about alignment. Hopefully someone could help me.
I collected data from two separate days and the localizer runs were only scanned in the first day. Now I'm trying to align all the data together, including anat scans, epi scans and also the masks (created with the localizers and the anat image of the first day). Here are the code and steps that I'm using ri
by
SarahChang
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AFNI Message Board