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--- neuroimagen:afni_proc [2020/01/28 09:54]
osotolongo [Del template a los scripts]
+++ neuroimagen:afni_proc [2020/01/31 22:20]
osotolongo [Resultados]
@@ Line 5: / Line 5: @@
 https://blog.cogneurostats.com/2013/05/29/single-subject-analysis-in-afni/
+**Revisar aqui primero:**
+https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/afni_proc.py_sphx.html
 ===== Construyendo el template =====
@@ Line 274: / Line 276: @@
 </code>
+===== Resultados =====
+Revisar esto visualmente con AFNI tiene truco,
+<code bash>
+[osotolongo@detritus mopead]$ cd afni_out/sub_0001.results/
+[osotolongo@detritus sub_0001.results]$ afni -dset all_runs.sub_0001+tlrc
+Thanks go to J Evans for useful feedback
+Initializing: X11.++ AFNI is detached from terminal.
+[osotolongo@detritus sub_0001.results]$ . Widgets...... Input files:
+ dataset count = 1
+ Time series   = 22 files read
+  NLfit & NLerr= Optimizer (AFNI_NLFIM_METHOD) is SIMPLEX
+  NLfit & NLerr= Found 26 models
+ Plugins       = 52 libraries read
+++ NOTE: This version of AFNI was built Sep 30 2013 ++
+++ NOTE: 'Define Markers' is hidden: right-click 'DataDir' to see it
+++ NOTE: you may want to consider creating a '.afnirc' file in your home
+         directory, to control AFNI's setup.  For more details, see
+   http://afni.nimh.nih.gov/pub/dist/doc/program_help/README.environment.html
+</code>
+{{ :neuroimagen:2020-01-29-103059_grim.png |}}
+**nota:** Necesito otro monitor mas!
+{{ :neuroimagen:2020-01-29-112733_grim.png |}}
+https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/afni_proc.py_sphx.html#main-outputs-many-datasets-are-created
+Para el //resting state//, el archivo de output con los datos limpios es //errts+sub_XXXX+tlrc//. Puedo convertirlo a formato NIfTI facilmente,
+<code bash>
+[osotolongo@detritus sub_0001.results]$ 3dAFNItoNIFTI -prefix sub_0001_fmri_clean errts.sub_0001+tlrc
+++ 3dAFNItoNIFTI: AFNI version=AFNI_2011_12_21_1014 (Sep 30 2013) [64-bit]
+[osotolongo@detritus sub_0001.results]$ fslinfo sub_0001_fmri_clean.nii
+data_type      FLOAT32
+dim1           54
+dim2           64
+dim3           50
+dim4           200
+datatype       16
+pixdim1        3.000000
+pixdim2        3.000000
+pixdim3        3.000000
+pixdim4        2.130000
+cal_max        0.0000
+cal_min        0.0000
+file_type      NIFTI-1+
+[osotolongo@detritus sub_0001.results]$ 3dAFNItoNIFTI -prefix sub_0001_anat pb03.sub_0001.r01.volreg+tlrc
+++ 3dAFNItoNIFTI: AFNI version=AFNI_2011_12_21_1014 (Sep 30 2013) [64-bit]
+[osotolongo@detritus sub_0001.results]$ fslinfo sub_0001_anat.nii
+data_type      INT16
+dim1           54
+dim2           64
+dim3           50
+dim4           200
+datatype       4
+pixdim1        3.000000
+pixdim2        3.000000
+pixdim3        3.000000
+pixdim4        2.130000
+cal_max        0.0000
+cal_min        0.0000
+file_type      NIFTI-1+
+[osotolongo@detritus sub_0001.results]$ fslview_deprecated sub_0001_anat.nii sub_0001_fmri_clean.nii -l "render1" -b 0,6 -t 0.7
+</code>
+{{ :neuroimagen:2020-01-30-114522_grim.png |}}
+{{ :neuroimagen:2020-01-30-160900_grim.png |}}
+{{:neuroimagen:recording.mp4|}}
+===== y ahora? =====
+Postprocessing,
+  * https://blog.cogneurostats.com/2013/04/09/using-r-with-afni/
+  * https://blog.cogneurostats.com/2014/03/25/r-for-mri-lovers-part-1/
+  * https://blog.cogneurostats.com/2014/09/03/r-for-mri-lovers-part-2/
+  * https://blog.cogneurostats.com/2013/07/24/creating-volume-rois-in-afni/

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