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 1 of 1 Pages: 1
Results 1 - 22 of 22
I am converting dcm to nii files. My dcm files are PET images from Siemens HRRT scanner. Somehow dcm2niix_afni doesn't recognize the name of manufactory in the header of dcm files, and gives out tons of warning messages (one warning each slice) like below:
Warning: Unknown Manufacturer CPS
Warning: Unknown Manufacturer CPS
.............(thousands of repeated warnings)....
Warning: Unknow
by
Juen
-
AFNI Message Board
Hi Rick,
I have tried -ushort2float last night. It didn’t work. It looks like this parameter just do the swapping with the expression “ step(a) *a + step(-a)*(a+65536)”. The output produced by Dimon has a range of 0 – 65229. However, the outputs produced by dcm2niix_afni or SPM has a range of 0 – 94914.53. Note that 94914 is much greater than 65536 (the max value of 16 bit short).
I have noti
by
Juen
-
AFNI Message Board
Thanks Daniel! It does seem a data swapping problem. The output from dcm2niix_afni does not have extreme low numbers in the hot spot. However, I have trouble running this command. It gives the following error message:
Dcm2niix_afni -o ./ ./dicom_dir
Found 621 DICOM files
Error: Instance number (0020, 0013) not found: ./dicom_dir
1 images have identical time, series, acquisition and image val
by
Juen
-
AFNI Message Board
Our group are using PET images to study dopamine receptors with AFNI. The receptors are highly concentrated in striatum; we usually see strong signals (values) in the entire region of striatum. In the first step of our analyses, we convert dicom files to AFNI files. However, I noticed that sometime there appear a few voxels with extremely low values in this hot region (striatum). These extreme va
by
Juen
-
AFNI Message Board
Yes, I have a similar question:
can I set individual voxel threshold pvalue larger than the claimed p-value for cluster? In another word, can I set p=0.1 and then claim a cluster significant at 0.05 if the size of that cluster is above the value given by 3dClustSim? Is it a legitimate approach or a kind of cheating?
Thanks,
Juen
by
Juen
-
AFNI Message Board
Hi AFNI,
I am using 3dUnifize to unifize anatomical MRI and then run 3dSkullStrip because my images are bright on top and dark on bottom. It works for most of my datasets. But I have got a couple of 'unifized' images with bottom half of cerebellum chopped off, probably because it is too dark on bottom. I have tried the two options "-GM and Urad", but couldn't solve the p
by
Juen
-
AFNI Message Board
Thanks Dr. Cox,
It does the trick.
I have been stuck with this problem for many days. It is a huge relief now.
Many many thanks!!!
Juen
by
Juen
-
AFNI Message Board
Hi AFNI,
Most of my anatomical images are darker on the bottom and lighter on the top. This issue makes 3dskullstrip difficult to completely cover temporal pole and cerebellum. When I used default option, the whole left temporal pole was chopped off sometime. Even when I used “3dSkullStrip -input l_s301_gfl_d1.anat_1+orig -prefix l_s301_ns -blur_fwhm 2 -use_skull -avoid_vent -push_to_edge -init
by
Juen
-
AFNI Message Board
Thanks to your suggestion, I just realized I missed "-input" in the command line. Now it is working.
Juen
by
Juen
-
AFNI Message Board
Hi,
I have got the following error message when I run 3dSkullStrip
Error SUMA_BrainWrap_ParseInput (SUMA_3dSkullStrip.c:1153):
But @auto_tlrc can give me a stripped skull with no problem. However I still want to run it separately.
(I just updated my afni and I don't use SUMA).
Any idea is welcome.
Juen
by
Juen
-
AFNI Message Board
Hi all,
I have a dataset (PET scans) with big displacement between subbricks. The 3dvolreg could not get all the subbricks lined up. I have considered doing a manual alignment with “Nudge Dataset” plugin. However, ‘Nudge’ doesn’t allow me to apply translation and rotation to individual subbrick.
I wonder if there is any command or plug in that can do this job.
Best,
Juen
by
Juen
-
AFNI Message Board
Hi Rick,
I tried your suggestion with the rever_org_dir option. It works. But it reverts not only the time order, but also the slice order in the dimon.files.run I could not see an effect of this reverse slice order when I view the volume in afni reviewer. But I am still worring about any potential effect of slice order. (I am a beginner in the afni community).
Best,
Juen
by
Juen
-
AFNI Message Board
Thanks Rick,
Nothing wrong with GERT_Reco or runnign the GERT. Actually it is the dimon.files.run has the wrong order of my dicom files (the wrong order is not just random order, it is actually the reverse order).
I always clean up old files before I run any new commands. It is unlikely to read the old file.
The problem must come from the Dimon command.
Anyway, I can use matlab to genera
by
Juen
-
AFNI Message Board
Hi Rick,
It seems like it runs ok if I run individual dimon command in terminal window.
But if I put multiple dimon, to3d in a script, the misorder happens again.
my script is like this:
#!/bin/tcsh
setenv AFNI_DICOM_RESCALE YES
dimon .....
./GERT_Reco_dicom*
cd ../another directory
dimon ..
./GERT_Reco_dicom*
exit 0
Juen
by
Juen
-
AFNI Message Board
Hi Rick,
That is the option I used at the beginning. Here is my line:
Dimon -infile_pattern '*.dcm' -dicom_org -GERT_Reco -quit
I have even tried: -use_last_elem -use_slice_loc -dicom_org -sort_by_acq_time. It does not work either.
Best,
Juen
by
Juen
-
AFNI Message Board
Hi all,
I am using Dimon to convert dicom files to afni file. My file names are like this: Image.4_12000.dcm and Image.8_3200.dcm. The first numbe in the filename is slice number while the second number is time. The dicom files are PET images from NIH PET department.
The file, dimon.files.run, generated by Dimon, always give a wrong time order.
Probably I need set up some environment variable
by
Juen
-
AFNI Message Board
Hi All,
I am converting dicoms (256*256 int16) into afni using to3d. Some negative intensities always show up in the final images (-32768).
I am pretty sure this is a datum type issue, but don't know how to fix it.
I used '-datum short/byte/float', and it doesn't work. Then I tried to3d '3D:0:0:256:256:....' but I do not how to put this option because I am usin
by
Juen
-
AFNI Message Board
Hi All,
I am using to3d to convert dicom file into afni files. The dicom files are PET images with 207 slices per volume from the PET department in Bethesda campus. When I open the converted file, there appears a black belt in the middle of the volume. I tried to run to3d GUI, it seems to3d is able to correctly read the paramters in the dicom header. Since the black belt is not completly dark, I
by
Juen
-
AFNI Message Board