I added explanations for the naming of all tract masks in a docs file

docs/tract_naming_help.txt

@@ -1,40 +1,112 @@
-CC_MOp(dilated)
-CC_MOp(dilated)_cut.tt
-CC_MOp_MOp.tt
-CC_MOp_MOp_cut.tt
-CC_Mos_Mos.tt
-CC_MOs_MOs_cut.tt
-CC_SSp_ll.tt
-CC_SSp_ll_cut.tt
-CC_SSp_ul.tt
-CC_SSp_ul_cut.tt
-Corpus Callosum tract masks zwischen jeweils der gleichen rechten und linken Cortex region als ROI: einmal mit beiden dilated MOp als ROI, mit beiden normal-sized Mop als ROI, mit beiden MOs als ROI, mit beiden SSp-ll als ROI und mit SSp-ul als ROI. Für jeden CC noch eine gecuttete Version (gecuttet hinter den jeweiligen ROI).
-
-
-CST_links_CC_cut
-CST_links_CCasROA
-CST_links_ROA_CC_fibers_cut
-CST_rechts_CC_cut
-CST_rechts_CCasROA
-CST_rechts_ROA_CC_fibers_cut
-
-
-Optic_tract_final.tt 
-Mit Optic chasm als Seed und LGN rechts und links als ROI
-
-
-Retikulospinal_tract_links
-Retikulospinal_tract_rechts
-Damit ist der corticoretikular tract gemeint. Dilated MOp als Seed und 
-
-Rubrospinal_tract_links_
-Rubrospinal_tract_rechts
-Damit ist der corticorubral tract gemeint. Dilated MOp als Seed und red nucleus als 
-
-
-Thalamocorticale_links_SSp_and_SSs_End
-Thalamocorticale_links_SSp_ll_and_ul_ROI.tt
-Thalamocorticale_links_SSp_ul_and_ll_End_0,2.tt
-Thalamocorticale_rechts_SSp_and_SSs_End
-Thalamocorticale_rechts_SSp_ll_and_ul_ROI.tt
-Thalamocorticale_rechts_SSp_ul_and_ll_End_0,2.tt
+Corticospinal tract (CST):
+Starts in the primary motor cortex (MOp) and traverses through internal capsule and pyramid, before continuing into the spinal cord
+
+CST_MOp-int-py_contralesional_CCasROA.nii (right)
+CST_MOp-int-py_ipsilesional_CCasROA.nii  (left)
+-> Dilated primary motor cortex (MOp) as Seed Region (without dilation no tracking results, see thesis for details), internal capsule (int) pyramid (py) both as ROI
+Atlas region of the corpus callous (CC) added as ROA. 
+
+
CST_MOp-int-py_contralesional_CCcut.nii
+CST_MOp-int-py_ipsilesional_CCcut.nii
+-> Dilated MOp as Seed Region and int and py as ROI, generated fibers were diverted by the pathway of the CC (regions of crossing fibers), CC fibers were all cut right behind the MOps.
+
+
CST_MOp-int-py_contralesional_selfdrawnROA+CCcut.nii
CST_MOp-int-py_ipsilesional_selfdrawnROA+CCcut.nii
+-> Dilated MOp as Seed Region and int and py as ROI. Added self-drawn ball as ROA at the point where fibers exited the Mop and continued into the CC. Remaining CC fibers were cut.
+
+
+
+
+
+
+
+Corpus callosum (CC):
+Interhemispheric connections between several cortex regions
+
+CC_MOp-MOp.nii
+-> left and right primary motor cortex (MOp) as ROI
+CC_MOp-MOp_cut.nii 
+-> same, but fibers cut right before leaving 
+
+
+CC_MOp-MOp_dilated.nii
+-> MOps were dilated several times, in order to generate a bigger CC pathway, left and right dilated MOp as ROI
+CC_MOp-MOp_dilated_cut.nii
+-> same, but fibers cut right before leaving dilated MOps
+
+
+CC_MOs-MOs.nii
+-> left and right secondary motor cortex (MOs) as ROI
CC_MOs-MOs_cut.nii
+-> same, but fibers cut right before leaving both MOs
+
+
CC_SSp_ll-SSp_ll.nii
+-> left and right primary somatosensory cortex for lower limb (SSp-ll) as ROI
+CC_SSp_ll-SSp_ll_cut.nii
+->same, but fibers cut right before leaving both SSp-ll
+
+
CC_SSp_ul-SSp_ul.nii
+-> left and right primary somatosensory cortex for upper limb (SSp-ul) as ROI
CC_SSp_ul-SSp_ul_cut.nii
+->same, but fibers cut right before leaving both SSp-ul 
+
+
+
+
+
+
+
+
+
+Corticoreticular tract (CReT):
+Tracking of the reticulospinal tract was not possible, that's why the CReT was tracked instead. 
+CReT starts in the MOp and ends in the reticular formation, the tegmental reticular nucleus (TRN) is a key nucleus in the reticular formation 
+
+
CReT_MOp-TRN_contralesional_CCcut.nii (right)
CReT_MOp-TRN_ipsilesional_CCcut.nii  (left)
+-> Dilated MOp as Seed region (tracking with non-dilated MOp did non yield any results). Adding TRN as end region : all fibers were again diverted by CC fibers -- CC fibers were all cut before leaving the MOp
+
+
+
+
+
+
+
+
+
+Corticorubral tract (CRuT):
+Tracking of the rubrospinal tract was not possible, that's why the CRuT was tracked instead. 
+CRuT starts in the MOp and ends in the red nucleus (RN)
+
+
CRuT_MOp-RN_contralesional_mirrored_CCcut.nii (right)
CRuT_MOp-RN_ipsilesional_CCcut.nii (left)
+-> Dilated MOp as Seed region (tracking with non-dilated MOp did non yield any results). Adding RN as ROI and as end region : no accurate tracking results -- Adapting tracking parameters: Increased step size from 0.01mm to 0.2mm and angular threshold from 50 to 70 degrees. Tracking results were okay, but all fibers were again diverted by CC fibers -- CC fibers were all cut before leaving the MOp
+Could only be generated on the ipsilesional side, mirrored along the x-axis and saved as contralesional tract.
+
+
+
+


Optic tract (OT):
+Starts in the optic chiasm (och) and traverses through the lateral geniculate nucleus (lgn) of the thalamus. The tract ends in the primary visual cortex (V1).
+
OT_och-lgn_lgncut.nii
+-> och as Seed region and left and right lgn as ROI, fibers were all cut behind the lgn
+Due to partial crossing of fibers at the optic chiasm to the other hemsiphere, one optic tract mask was created for both sides together.
+
+
+
+
+
+
+Thalamocortical tract (TC) : 
+We wanted to track the tract seeding in the dorsal sensory-motor cortex related thalamus (DORsm) and ending in the primary somatosensory cortex for upper and lower limb (SSp-ul/ll)
+
TC_DORsm-SSp_ll+SSp_ul_contralesional_END+higherstepsize.nii (right)
+TC_DORsm-SSp_ll+SSp_ul_ipsilesional_END+higherstepsize.nii.nii (left)
+-> DORsm regions (VPL, VPM, VAL) were merged and set as Seed region, SSp-ll and SSp-ul were merged and set as end region: No tracking results! Increased step size on 0.2mm : Fiebers were generated.
+
+
+
+
TC_DORsm-SSp_ll+SSp_ul_contralesional_ROI+CCcut.nii 
TC_DORsm-SSp_ll+SSp_ul_ipsilesional_ROI+CCcut.nii
+-> DORsm regions (VPL, VPM, VAL) were merged and set as Seed region, SSp-ll and SSp-ul were merged and set as ROI, CC fibers were cut
+
+
+
+
TC_DORsm-SSp+SSs_contralesional_END+CCcut.nii
TC_DORsm-SSp+SSs_ipsilesional_END+CCcut.nii
+-> -> DORsm regions (VPL, VPM, VAL) were merged and set as Seed region, and the primary and secondary somatosensory cortex (SSp and SSs) were merged and set as end region. All CC fibers were cut
+
+
+
+For more details see bachelor thesis