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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
Page 4 of 5
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Results 91 - 120 of 136
Hi Peter,
Thanks for the suggestion. In case it is helpful for others, the Freesurfer group mentioned using -xhemi options to perform the flip. DO NOT use mri_reverse.
Best,
Ajay
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AjaySK
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AFNI Message Board
Hi Bob,
Thanks for the quick reply. I am looking at some brains with very abnormal ventricles while other brain structures within the same brain are normal size. I was trying to figure out how to allow 3dQwarp larger warps in the ventricle areas while restricting the rest to more moderate warps.
(1) As for the -weights option I was trying to figure out it was just a scale or if I need
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AjaySK
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AFNI Message Board
Hello Afni experts,
I have 2 questions regarding how 3dQwarp works.
The first pertains to the -weight option where we can supply our own weights. What are the units that is expected for weights? Is this a 3d volume with mm shift for each direction with +/- for direction or is this an arbitrary weighting normalized to a scale between 0 and 1 or something else?
The second questio
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AjaySK
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AFNI Message Board
Hello Afni Experts,
I used 3dAllineate -cmass -1Dmatrix_save to align two images and it did a great job. I want to apply this transform to another image using 3dAllineate -1Dmatrix_apply however it does not apply the transform to align centers called by -cmass. Additionally, this transform for aligning centers is not saved anywhere. Is there any way to save out a complete transform which i
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AjaySK
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AFNI Message Board
Hi Peter,
Thanks again for the help. I have one follow up question. For some subjects I need to flip the hemisheric cortical thickness data so that all subjects have the same side affected. Since all of the subjects are warped to a custom fsaverage which is symmetric, what would be the best way to get the cortical thickness files flipped? Normally I would do something like 3dLRflip for vo
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AjaySK
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AFNI Message Board
Hi Peter,
Thanks for the speedy reply. I have run fsaverage through @SUMA_Make_Spec_FS. I have questions for each of the two options you gave me.
1) You said I can take the smoothed fsaverage warped thickness file ( Subject01.lh.thickness.fsaverage.gii) and do an analysis with 3dttest++. My question is do I have to first use MapIcosahedron on this file prior to the analysis? I would as
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AjaySK
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AFNI Message Board
Hi Afni Experts,
I was having an issue with converting all of my surface files from freesurfer to SUMA format. I wanted to see what are the manual commands necessary for a group analysis in case i cannot get suma_make_spec_fs working with my files (or what I need to modify).
I have a subjects native files in FS/mri and FS/surf folder.
Using the -qcache option I also have created the
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AjaySK
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AFNI Message Board
I just wanted to follow up with the 5x5x5 patch size issue as I am back on this step again. I wasn't sure if there were any updates or fixes for this issue, or if a new update to 3dQwarp was rolled out over that past few weeks?
Thanks,
Ajay
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AjaySK
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AFNI Message Board
Hi Rick and Peter,
This crash course in surface based analysis helped alot in clearing up my questions regarding suma tools and integration with Freesurfer.
For a vertex-wise analysis can I supply my native space brain cortical thickness files (after I smooth them with surfsmooth) which have been imported with SUMA_Make_Spec_FS (standardized mesh which matches my MNI template standardiz
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AjaySK
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AFNI Message Board
Hi Peter,
Thanks for the clarification. As i mentioned in my post to Rick I was thinking of modifying the script to use nonlinear transforms from 3dQwarp as a possible work around and use MNI template as my reference and the subject brain mesh as my source.....I was curious if you had any thoughts to this approach?
Thanks,
Ajay
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AjaySK
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AFNI Message Board
Hi Rick,
Thanks! I definitely would be interested in hearing about if SurftoSurf could be used for this procedure and how it works (is there any paper regarding how it works?). I was planning on taking my MNI template and running it through Mapsiconahedron as well as all native brain meshes such that they have the exact same number of nodes. I just am not sure of the details of how it woul
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AjaySK
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AFNI Message Board
Hi Rick,
Just thought I'd follow up with my previous questions:
1) Mapsaiconahedron uses affine warping?
2) In looking at the SUMA_AligntoExperiement command it uses 3dWarpDrive and 3dAllineate for warping my native brain surface to MNI. Do you see any issues if I replaced these command lines with nonlinear afni tools (ie 3dQwarp) to perform the nonlinear warp instead or is this no
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AjaySK
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AFNI Message Board
Hi Rick,
Thank you so much for the explanation.
So essentially if I use @SUMA_MAKE_SPEC_FS it will automatically call the Mapicosaohedron which will take your standard icosahedron shape and AFFINELY warp it to the native brain subject, correct?
1)Are all surface tools such as SurftoSurf and 3dVol2surf affine transforms (based on your response above), and if so are there any tools ex
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AjaySK
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AFNI Message Board
Hi Peter,
Thanks for the info. I was actually interested more in a hybrid approach and he second option which is running a surface based analysis for cortical regions as well as volumentric analysis for subcortical regions.
I wanted to take my native space brains and warp to MNI space. 3dQwarp does an exceptional job for subcortical regions and I wanted to take advantage of surface gy
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AjaySK
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AFNI Message Board
Thank you for your responses Peter and Rick.
Just to clarify, the processes would be the following:
1) Take the desired MNI template and run through freesurfer's autorecon process for generating surfaces and template sphere.
---- Do we need to (or should we ) use MapIcosahedron for anything at this step?
---- I assume this would be optional for MNI templates but then again I cou
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AjaySK
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AFNI Message Board
Hello Afni users,
I was also interested in how to incorporate some of these changes into SUMA? Any advice would be much appreciated.
Thanks,
Ajay
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AjaySK
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AFNI Message Board
Hello AFNI experts,
I had a problem when running auto_warp.py and wanted to see if you could help. According to the documentation, for 3dQwarp the smallest patch size accepted is 5mm.
-minpatch mm = Set the minimum patch size for warp searching to 'mm' voxels.
*OR* * The value of mm should be an odd integer.
-patchmin mm * The default value of mm is 25.
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AjaySK
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AFNI Message Board
Hi Rick,
I just wanted to follow up with TSNR regarding one of the lines of code for the calculation:
1) 3dTproject -polort 0 -input all.runs.$sub.pb04+orig -censor $out_dir/censor_${sub}_combined_2.1D -cenmode ZERO -ort
$out_dir/X.nocensor.xmat.1D -prefix errts.$sub.tproject.pb04
2) 3dTstat -stdev -prefix rm.noise.all.pb04 errts.$sub.tproject.pb04+orig
On the first line of code the
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AjaySK
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AFNI Message Board
Hi Afni experts,
I was interested in warping my subjects to MNI space using the ICBM 2009c nonlinear asymmetric template. In using the "whereamI" function I noticed that the labels are derived from the Collins 27 brain using Eickhoff-Zilles labels which overlay well for the most part. Since the template I am using and the MNIa_caez label file is not exactly the same shape in all r
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AjaySK
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AFNI Message Board
Hello AFNI experts,
I received the following bug when running afni_proc.py on a MacOSx 10.9.5 with the latest afni binaries:
3dDespike -NEW -nomask -prefix pb01.CON_020.r01.despike pb00.CON_020.r01.tcat+orig
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Applications/afni/3dDespike
Reason: image not found
Trace/BPT trap
Finished!
I followed previou
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AjaySK
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AFNI Message Board
Hi Rick,
Thanks for the help. I was hesitant using the -demean function due to the fact that the mean changes from region to region across the brain mask. I think that if I create a mask of each separate region and then apply the 3ddot with -demean option this should probably address those concerns.
Could another option be to actually create a voxelwise mean map (ie 3dLocalStat) of eac
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AjaySK
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AFNI Message Board
Hello Afni experts,
I wanted to find out the best way to get a correlation (pearson ideally) between two data sets. The 2 datasets are the same subject (native space) with the voxels of one image filled with STDEV values of a measure and the other image filled with %signal change. There is only one subbrick per dataset (not timeseries data).
I wanted to see if 3ddot with the demean opti
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AjaySK
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AFNI Message Board
Hi Afni experts,
I had a question with how to best combine obliquity information. I have an anatomical scan while was taken at oblique angle A and EPI which is taken at oblique angle B. I ran my anatomicals through Freesurfer and used bbregister to align the two images, which worked fine in their viewer.
Initially I loaded the aligned anatomical scan and original EPI in the viewer and
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AjaySK
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AFNI Message Board
Hi Rick,
I see the issue. I had set the template to warp to as MNI_avg152T1 image which is LPI whereas the MNI152_1mm_uni template is RPI (first template that comes up from MNI152 in the afni folder). Which template is better to use with 3dQWarp? Are there any modalities in which one is preferred to the other?
Also in regards to the original question which was about the warp field fil
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AjaySK
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AFNI Message Board
Hi Afni experts,
Just as a separate question related to 3dQwarp as it may be a potential bug...
My anatomical and rsfmri scans are both RPI (using 3dinfo) and the AFNI MNI152 template that I warp to (3dQwarp) is also shown as -RPI using 3dinfo, however the output brain+tlrc is showing as LPI format? This may be a bug as both the inputs and template show RPI format and the MNI version of th
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AjaySK
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AFNI Message Board
Hi Afni Experts,
I was interested in warping a subjects EPI data to T1 image (Limited to Level=1 so not overwarped) however when I looked at the X Y and Z components of the deformation fields they were not what I expected. Having used 3dQWarp for warping T1 images to MNI space I can generally make out gross anatomical boundaries and the warp fields look similar to the shape of the brain. Ho
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AjaySK
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AFNI Message Board
Hello Afni Experts,
I had a question regarding the pipeline as I also had data that I preprocessed on my own.
1) My EPI images are in RPI orientation so is it necessary to run 3daxialize/3drefit -deoblique? The images were taken at an oblique angle but I have all of my masks/anatomicals already aligned to the EPI and so is this necessary? If it is necessary, since my images are in RPI
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AjaySK
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AFNI Message Board
Hi Afni Experts,
I wanted to use custom slicetime file in order to apply physio correction to multiecho data (supply 1D file) and then apply the same pattern to 3dTshift (via afni_proc.py). Additionally I wanted to correct TR in the header.
1) Does RetroTS(or MCRetroTS) uses TR in units of seconds and expects the custom sliceorder to also be in units of seconds (column format)?
I use
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AjaySK
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AFNI Message Board
Hi Rick,
When looking at the output of afni_proc.py I used history to look at how the TSNR images are created and found the following:
3dTcat -prefix all.runs.$sub.pb04 $out_dir/pb04.$sub.r01.volreg+orig
3dTstat -mean -prefix rm.signal.all.pb04 all.runs.$sub.pb04+orig
3dTproject -polort 0 -input all.runs.$sub.pb04+orig -censor $out_dir/censor_${sub}_combined_2.1D -cenmode ZERO -ort
by
AjaySK
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AFNI Message Board
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Pages: 12345