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
Hi Taek-
You'll need to make the cuts on the inflated maps in Freesurfer. You can follow the tutorials on any of these sites:
1.
2.
3.
The first one includes the commands in AFNI to use. To view that, you can add the lines into the .spec files that AFNI will use. I have a vague recollection that if you name the cut and flattened surfaces correctly, @SUMA_Make_Spec_FS will auto
by
Peter Molfese
-
AFNI Message Board
I'm pretty happy with the performance of my 13" Macbook Pro (MBP) with touch bar. The 3.1Ghz model is a big jump in technical specs for not a huge amount of additional costs. The 16GB of memory is certainly useful depending on what you're running, and data is constantly getting bigger (multi-band, multi-echo, etc) - so some amount of "future proofing" is good if you can
by
Peter Molfese
-
AFNI Message Board
You can run @update.afni.binaries -d
This can be done as a cron on most systems. You can decide if you want that daily, weekly, monthly. AFNI updates happen with some regularity - which could mean daily or weekly.
by
Peter Molfese
-
AFNI Message Board
I usually place it in /usr/local/abin so that all users can access it.
The advantage of each user installing it in their own home directory is that they can then be in charge of when updates are installed. We generally recommend using the most recent version whenever possible, so perhaps this is less of an issue.
by
Peter Molfese
-
AFNI Message Board
The value in AFNI isn't in millimeters or degrees (or radians) of rotation. So using the "same" value as other software packages is fairly meaningless. You can approximate, but if you wanted roughly 3mm or 3 degrees, than you want a value of ~ 0.3 for AFNI.
If you don't want to do ANY type of motion correction, then you can remove the "volreg" block from AFNI.
by
Peter Molfese
-
AFNI Message Board
-regress_censor_motion 3.0
Should be
-regress_censor_motion 0.2
by
Peter Molfese
-
AFNI Message Board
Worth verifying with your scan center, but I believe your timing should be "alt+z2" for even number of slices. Depending on which scanner, which software version, and which sequence of course. The incorrect timing information on slice time correction could play decent havoc on your analyses. Particularly with such a large TR window.
Also, as Bob mentioned a censor threshold of 3
by
Peter Molfese
-
AFNI Message Board
Ok, I'm guessing that you're using a Siemens scanner? My first guess is that the slice timing information isn't included in the DICOM headers, so you need to specify it to afni_proc.py using something like this:
-tshift_opts_ts -tpattern alt+z
The default on Siemens is to use alt+z with odd number slices and alt+z2 on even number slices.
Whereas all the other packages re
by
Peter Molfese
-
AFNI Message Board
It would be helpful to post the entire afni_proc.py command used in your analyses. I'm assuming that you're running two processing pipelines, one for MOCO and one for NOTMOCO.
-Peter
by
Peter Molfese
-
AFNI Message Board
Hi Paul-
My inclination is to recommend Option 1, compute a summary statistic and then use that for your prediction. I think the variability of using all of the data points is going to make classification difficult. I can't promise that RSFC measures will be the answer, but that seems like a better option than all of the issues you may have using "raw" time series.
Happy
by
Peter Molfese
-
AFNI Message Board
If you use afni_proc.py for your analyses, you shouldn't need to worry about oblique data differences, as they will (under most circumstances) be handled by the script. It will also handle all of your other preprocessing needs!
There's a nice introduction here.
by
Peter Molfese
-
AFNI Message Board
Hmm... That program (siemenstoafni) is really old and not part of the AFNI distribution. You can see this thread. I'd recommend using the AFNI program Dimon or dcm2nii. There's a handy blog post on this as well.
As for processing, we recommend that users take a look at the "new" afni_proc.py script included in the distribution. The class handouts from bootcamps are he
by
Peter Molfese
-
AFNI Message Board
I suspect having multiple -align_opts_aea is why you are not seeing the -giant_move option executed. I believe that you could use a combination of --tlrc_anat, -volreg_tlrc_adwarp, and -volreg_warp_dxyz to perform what you want in afni_proc.py.
If you're willing to use the nonlinear transform, you can use auto_warp.py once and then apply that transform to all of your afni_proc.py calls
by
Peter Molfese
-
AFNI Message Board
If you don't specify either, the program uses the default mentioned above. If you add the -verbose flag to the command it will output what the "common time point" is set to. In afni_proc.py, the default is to use a -tzero 0 (align to the first).
by
Peter Molfese
-
AFNI Message Board
Hi,
You could specify a slice as the reference using the -tzero or -slice options. But the default is to use the average.
The default alignment time is the average
of the 'tpattern' values (either from the
dataset header or from the -tpattern option)
by
Peter Molfese
-
AFNI Message Board
There's quite a few possibilities here. One that comes to mind immediately is to use 3dRSFC to extract summary statistics (e.g. ALFF) from resting state data to use in the SVM.
Likely someone has done something similar to what you're aiming to do, and you could use a similar analysis.
by
Peter Molfese
-
AFNI Message Board
You can use 3drefit to change the header of the NIFTI files (or of AFNI files). I usually go for double when I'm converting odd headers:
3drefit -view orig -space ORIG myFile.nii.gz
by
Peter Molfese
-
AFNI Message Board
I suspect that some of your input files are incorrectly labeled as being in standard space (+tlrc) in the NIFTI header. You can check this using 3dinfo.
I find it useful to explicitly define the blocks using a -blocks or -do_blocks command in afni_proc.py. Also if you want all of your data to end up in standard space, you likely want a -volreg_tlrc_warp in your command.
We usually sug
by
Peter Molfese
-
AFNI Message Board
Worth checking what Dimon says, try running the following and posting the results:
Dimon -infile_pattern *.dcm -gert_create_dataset -dicom_org
by
Peter Molfese
-
AFNI Message Board
If the GUI is popping up, it usually means that something in your command line isn't specified and the GUI is asking you for help. Please post your command and describe what you're converting from DICOM to NIFTI.
Alternatively, you can use dcm2niix_afni which is now included in the binaries for quick conversion.
-Pete
by
Peter Molfese
-
AFNI Message Board
You should feed afni_proc.py the three runs after the -dsets flag. Your timing files are then one row per run starting at time 0 for each run. afni_proc.py and relevant commands will figure it out from there!
You have the option to specify what we call "global" times as well, but the local method (described above) is usually more straightforward.
-Peter
An example of a rec
by
Peter Molfese
-
AFNI Message Board
I would not concatenate your data before feeding it into afni_proc.py. It's not uncommon for different scanner runs to have slightly different values (arbitrary units). The scale step would turn each of those runs into a % signal change that would then be comparable.
Feel free to post your afni_proc.py command for further insights!
by
Peter Molfese
-
AFNI Message Board
There is a program called 3dkmeans that may meet your needs.
by
Peter Molfese
-
AFNI Message Board
That's correct, 3dTshift does not know the slice order if they aren't transcribed into the header. This is actually pretty common with conversion of DICOMs to NIFTI via dcm2nii or other tools.
You should use the syntax for explicitly setting the slice order, just make sure to use the correct order:
-tshift_opts_ts -tpattern seq-z
Alternatively, you can set the slice order u
by
Peter Molfese
-
AFNI Message Board
Absolutely! Checkout SurfToSurf. If you made the surfaces in @SUMA_Make_Spec_FS, you likely have the mapping file you need already (M2M).
-Peter
by
Peter Molfese
-
AFNI Message Board
One solution is to first use ROI2dataset with the -pad_to_node option on your ROI then run 3dmaskdump/3dmaskave/3dROIstats.
-Pete
by
Peter Molfese
-
AFNI Message Board
Hello,
3dANOVA3 can only handle fully balanced designs. You should try using 3dMVM .
-Pete
by
Peter Molfese
-
AFNI Message Board
For a standard transform, you need to specify the conversion mapping. Consider the following example from the help for MapIcosahedron:
SurfToSurf \
-i_fs std.60.rh.smoothwm.asc \
-i_fs rh.smoothwm.asc \
-prefix std.60. \
-mapfile std.60.rh.niml.M2M \
-dset rh.SOMEDSET.gii.dset
What's the main reason to map to the Freesurfer sphere space? The standard mesh is already comparable
by
Peter Molfese
-
AFNI Message Board
Occasionally text files and scripts get a bit clobbered. My usual troubleshooting is to open the script with TextWrangler, and check to see if you see hidden characters. You can also use the program to save as plain text and set the new line character as Linux/Unix.
-Pete
by
Peter Molfese
-
AFNI Message Board
Installing AFNI would be the most supported way of doing things. But if you're really trying to avoid it, here's a couple of options:
1. AFNIpy and Nibable could likely do the work
2 Freesurfer's mri_convert looks like it could do the trick.
by
Peter Molfese
-
AFNI Message Board