Show all posts by user
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 3 of 3
Pages: 123
Results 61 - 83 of 83
Thank you Rick. I ran @SSwarper and the jpeg files look reasonable. When I tried to feed the inputs back into my afni_proc.py script however, it resulted in an error message indicating that the +tlrc warp dataset was missing. It seems afni_proc.py was trying to find the file "anatQQ.MNI152_2009_template_SSW.nii.gz+tlrc" which I don't have.
Would it be safe to replace the ending
by
tamtam
-
AFNI Message Board
Great, thank you! The subject's ventricles is fairly large -this person does have quite a bit of atrophy. I will keep these tips in mind as I go through the remaining scans.
Thank you again for you assistance.
Best,
Tamara
by
tamtam
-
AFNI Message Board
Hello,
I ran @SSwarper on the two subjects with poor skull stripping.. I ran the following code and the program seemed to run successfully:
@SSwarper \
11916.anat+orig \
MNI152_2009_template_SSW.nii.gz \
11916
I was reading online that the two JPEG files should be inspected to ensure that the skull-stripping and non-linear warping worked. For these, do I just ensure (1) there is no skul
by
tamtam
-
AFNI Message Board
Great! I may switch to @SSwarper depending on what the skulls look like. Thank you for your help!
by
tamtam
-
AFNI Message Board
Thank you for the information. I have already processed 30+ participants through the non-linear warping route in afni_proc.py so I may want to keep utilizing the 2009c template for consistency. Are there other ways I can try to fix the skull stripping?
Thank you,
Tamara
by
tamtam
-
AFNI Message Board
Thank you for the information! I will try this.
I have been using MNI152_T1_2009c+tlrc as the base in my afni_proc.py script. I notice that @SSwarper offers the MNI152_2009_template_SSW.nii.gz template. Are there any differences between these two templates? Are there potential problems if I use the "2009" template on 2-3 participants and the "2009c" template on the rest?
by
tamtam
-
AFNI Message Board
Hello,
I am currently using afni_proc.py to complete my pre-processing, and as I was completing my quality checks, I noticed that chunks of two participant's brains were removed during skull stripping. I used the various options indicated in 3dSkullStrip to help alleviate this problem but this did not help. Are there any other suggestions I can try? I have attached a copy of the resulting
by
tamtam
-
AFNI Message Board
Hi Rick,
Just an additional follow-up question, what do the Y-axis on the X.stim.xmat.1D and Sum_ideal.1D represent? Are these just arbitrary numbers?
Thank you for your help!
Best,
Tamara
by
tamtam
-
AFNI Message Board
Thank you for the recommendation! I began running this analysis when the binaries were updated, so I am a bit worried about updating them now as I am in mid-analysis. Do you think I should still update them? Would it be recommended for me to re-run my analysis again?
I've also pasted a picture of the anatomical scan in case you wanted to look at the movement.
I have pasted my script b
by
tamtam
-
AFNI Message Board
Hello,
I have a question regarding an error related to affine transformations (see error message below). Upon inspection I saw that this participant's anatomical scan has a lot of movement -it is very blurry and "grainy". I have attempted to rectify the error by following the suggestion in a related post by skipping the affine step using "-affine_input_xmat ID"; howeve
by
tamtam
-
AFNI Message Board
Hello,
As suggested by my AFNI readings, I have been using the @ss_review_driver to check the accuracy of the pre-processing outputs. I have gone through these outputs and the related readings, and I have a few questions regarding what I should be specifically checking at each stage. I am attempting to ensure my outputs are correct and accurate, so I appreciate any clarifications and further r
by
tamtam
-
AFNI Message Board
Hello,
Based on AFNI message board recommendations, I am attempting to tlrc my anatomical data to MNI template (2009c version) using auto_warp. I have successfully completed this in the GUI using the "@auto_tlrc" option, but when I try to use "auto_warp" in the GUI I receive the following error:
cat_matvec 10404.anat_ns+tlrc::WARP_DATA -I
ERROR:[0m THD_read_dvecmat:
by
tamtam
-
AFNI Message Board
Hello,
I manually tlrc my anatomical images and ran the uber_subject.py to pre-process the data. In the GUI I checked off "include copy of anat+tlrc" in the "anatomical dataset" section, so the +tlrc version can be included. When I ran my script, there was an error message regarding finding a specific file: "** FATAL ERROR: can't open -base dataset 'final_ep
by
tamtam
-
AFNI Message Board
Hello,
I manually tlrc my anatomical images and ran the uber_subject.py to pre-process the data. In the GUI I checked off "include copy of anat+tlrc" in the "anatomical dataset" section, so the +tlrc version can be included. When I ran my script, there was an error message regarding finding a specific file: "** FATAL ERROR: can't open -base dataset 'final_epi
by
tamtam
-
AFNI Message Board
Thank you for your reply and your help.
In the uber_subject GUI, can I just substitute the "MNI_avg152T1_tlrc" for either MNI_N27+tlrc or MNI152_2009_template (I am not 100% sure if those are the correct names of the templates you were referring to)?
Thank you in advance for your assistance.
Best,
Tamara
by
tamtam
-
AFNI Message Board
Hi All,
I am using the GUI to pre-processing my scans and have selected to automatically tlrc my data into the MNI_avg152 space. Currently, I am working with a data set comprised of patients and controls, where the patients demonstrate some atrophy (some more than others). I was wondering whether manual vs. auto tlrc may result in more accurate aligning, especially for my patients with atrophy
by
tamtam
-
AFNI Message Board
Great, thank you for clarifying. I see in the resulting script from uber_subjects that my polort is "3". So a cubic term is used.
Thank you again.
Tamara
by
tamtam
-
AFNI Message Board
Hi Rick,
Thank you for your response. Just to clarify, what does "trend" refer to? Does it refer to the mean raw signal or the trend that was computed to de-trend the data?
Thank you for your help.
Tamara
by
tamtam
-
AFNI Message Board
Hello,
I am working through the AFNI tutorials for pre-processing and I have a question regarding the "auto block: outcount" procedure. It indicates that "at each voxel, the data is detrended using the default polynominal degree based on the duration of the first run. For that voxel time series, any value that is too far from the trend is considered an outlier."
Does thi
by
tamtam
-
AFNI Message Board
Thank you for your help!
I ran the uber_subjects.py with the settings you suggested and I received the following error that I am not sure I understand:
[7m** FATAL ERROR:[0m '-stim_times 1' file 'stimuli/NonRevP_learn_corr_fed.txt' has 1 auxiliary values per time point
I am not sure what is meant that my regressors have auxiliary values. I should mention that my r
by
tamtam
-
AFNI Message Board
Hello,
I have a question regarding censoring vs. regressing motion derivatives in the uber_subject.py. Does it make sense to censor motion AND regress motion derivatives, or should I only complete one? My concern would be that even after TRs with lots of movement has been censored, other TRs with movement remain, which can impact the quality of my data?
Thank you so much for your help.
B
by
tamtam
-
AFNI Message Board
Hello!
I am relatively new to fMRI analysis and AFNI, and have been spending a good chunk of time working through the AFNI bootcamp workshops online and the "Class Handouts". I have a question regarding the uber_subject.py script I was hoping to get some help with.
For my task, I have my stimulus (jittered duration 2500ms, 4000ms or 5500ms) and then my feedback screen (1500ms).
by
tamtam
-
AFNI Message Board
Page 3 of 3
Pages: 123