Vesa Kiviniemi

22 papers Journal 19Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
NeuroImage
Joanne Wardell, Kseniya Solovyeva, David Danks, Niko Huotari, Vesa Kiviniemi, Vesa Korhonen, Thomas DeRamus, Godfrey D. Pearlson, Vince D. Calhoun, Sergey M. Plis
2026 J jnl
NeuroImage
Katariina Laurén, Matti Järvelä, Niko Huotari, Lauri Raitamaa, Janne Kananen, Johanna Tuunanen, Tommi Väyrynen, Vesa Korhonen, Katariina Hautamäki, Tuula Hurtig, Marja-Leena Mattila, Katja Jussila, Vesa Kiviniemi
2025 J jnl
NeuroImage
Anssi Koivula, Vilma Perkiömäki, Mika Aho, Aleksi Rasila, Valter Poltojainen, Vesa Korhonen, Matti Järvelä, Niko Huotari, Heta Helakari, Johanna Tuunanen, Lauri Raitamaa, Tommi Väyrynen, Johanna Kruger, Vesa Kiviniemi, Janne Kananen
2025 J jnl
NeuroImage
Saara Sofia Syväoja, Lauri Raitamaa, Heta Helakari, Jussi Kantola, Matti Järvelä, Janne Kananen, Ville Isokoski, Vesa Korhonen, Tommi Väyrynen, Timo Tuovinen, Jürgen Hennig, Vesa Kiviniemi
2020 J jnl
NeuroImage
Lassi Björnholm, Juha Nikkinen, Vesa Kiviniemi, Solja Niemelä, Mark Drakesmith, C. John Evans, G. Bruce Pike, Louis Richer, Zdenka Pausova, Juha Veijola, Tomás Paus
2019 J jnl
IEEE Trans. Medical Imaging
Zalan Rajna, Lauri Raitamaa, Timo Tuovinen, Janne Heikkilä, Vesa Kiviniemi, Tapio Seppänen
2018 J jnl
NeuroImage
Jaakko Paasonen, Petteri Stenroos, Raimo A. Salo, Vesa Kiviniemi, Olli Gröhn
2017 J jnl
NeuroImage
Ville Raatikainen, Niko Huotari, Vesa Korhonen, Aleksi Rasila, Janne Kananen, Lauri Raitamaa, Tuija Keinänen, Jussi Kantola, Osmo Tervonen, Vesa Kiviniemi
2017 J jnl
NeuroImage
Lassi Björnholm, Juha Nikkinen, Vesa Kiviniemi, Tanja Nordström, Solja Niemelä, Mark Drakesmith, C. John Evans, G. Bruce Pike, Juha Veijola, Tomás Paus
2016 J jnl
Neural Comput.
Aapo Hyvärinen, Junichiro Hirayama, Vesa Kiviniemi, Motoaki Kawanabe
2016 conf
HEALTHINF
Angelos Fylakis, Anja Keskinarkaus, Vesa Kiviniemi, Tapio Seppänen
2015 conf
ISMICT
Angelos Fylakis, Anja Keskinarkaus, Vesa Kiviniemi, Tapio Seppänen
2015 conf
EMBC
Zalan Rajna, Anja Keskinarkaus, Vesa Kiviniemi, Tapio Seppänen
2014 J jnl
Brain Connect.
Vesa Korhonen, Tuija Hiltunen, Teemu Myllylä, Xindi Wang, Jussi Kantola, Juha Nikkinen, Yufeng Zang, Pierre LeVan, Vesa Kiviniemi
2013 J jnl
NeuroImage
R. Matthew Hutchison, Thilo Womelsdorf, Elena A. Allen, Peter A. Bandettini, Vince D. Calhoun, Maurizio Corbetta, Stefania Della Penna, Jeff H. Duyn, Gary H. Glover, Javier Gonzalez-Castillo, Daniel A. Handwerker, Shella D. Keilholz, Vesa Kiviniemi, David A. Leopold, Francesco de Pasquale, Olaf Sporns, Martin Walter, Catie Chang
2012 J jnl
J. Sensors
Teemu Myllylä, Vesa Korhonen, Erkki Vihriälä, Hannu Sorvoja, Tuija Hiltunen, Osmo Tervonen, Vesa Kiviniemi
2011 J jnl
Brain Connect.
Vesa Kiviniemi, Tapani Vire, Jukka J. Remes, Ahmed Abou Elseoud, Tuomo Starck, Osmo Tervonen, Juha Nikkinen
2011 J jnl
NeuroImage
Jukka J. Remes, Tuomo Starck, Juha Nikkinen, Esa Ollila, Christian F. Beckmann, Osmo Tervonen, Vesa Kiviniemi, Olli Silvén
2009 J jnl
Frontiers Neuroinformatics
Vesa Kiviniemi, Jukka J. Remes, Tuomo Starck, Juha Nikkinen, Marianne Haapea, Olli Silvén, Osmo Tervonen
2005 J jnl
NeuroImage
Minna Mäkiranta, Jyrki Ruohonen, Kalervo Suominen, Jaakko Niinimäki, Eila Sonkajarvi, Vesa Kiviniemi, Tapio Seppänen, Seppo Alahuhta, Ville Jäntti, Osmo Tervonen
2004 J jnl
NeuroImage
Minna Mäkiranta, Jyrki Ruohonen, Kalervo Suominen, Eila Sonkajarvi, Timo Salomäki, Vesa Kiviniemi, Tapio Seppänen, Seppo Alahuhta, Ville Jäntti, Osmo Tervonen
2003 J jnl
NeuroImage
Vesa Kiviniemi, Juha-Heikki Kantola, Jukka Jauhiainen, Aapo Hyvärinen, Osmo Tervonen
redb/extractors/pe_extractors/pe_dotnet.py
← Index redb/extractors/pe_extractors/pe_dotnet.py python
import inspect
import pefile
from dotnetfile import DotNetPE

import base64
from hashlib import md5
from pprint import pprint

import magic
import pefile

from redb.extractors.enum import Tag
from redb.extractors.pe_extractor import PEExtractor
from redb.models.dataclasses import PEDotNet
from datetime import datetime, timezone
import json
from typing import Any


class PEDotNetExtractor(PEExtractor):

    def __init__(
        self,
        filepath,
        log,
        exporters=None,
        index_prefix=None,
        elastic_index=None,
        known_benign=False,
        known_malicious=False,
        pe=None,
    ):
        super().__init__(
            filepath,
            log,
            exporters,
            index_prefix,
            elastic_index,
            known_benign,
            known_malicious,
            pe,
        )
        # self.pe_features = None
        self.elastic_index = self.index_prefix + "-pe_dotnet"
        self.dotnet, self.error = self._generate_dotnetfile_object()
        self.log.debug(inspect.currentframe().f_code.co_name)

    def _decode_assembly_flags(self, flag_value):
        self.log.debug(inspect.currentframe().f_code.co_name)
        ASSEMBLY_FLAGS = {
            0x00000001: "COMIMAGE_FLAGS_ILONLY",
            0x00000002: "COMIMAGE_FLAGS_32BITREQUIRED",
            0x00000004: "COMIMAGE_FLAGS_IL_LIBRARY",
            0x00000008: "COMIMAGE_FLAGS_STRONGNAMESIGNED",
            0x00000010: "COMIMAGE_FLAGS_NATIVE_ENTRYPOINT",
            0x00010000: "COMIMAGE_FLAGS_TRACKDEBUGDATA",
            0x00020000: "COMIMAGE_FLAGS_32BITPREFERRED",
        }
        flags = []
        for bit, name in ASSEMBLY_FLAGS.items():
            if flag_value & bit:
                flags.append(name)
        return flags

    def _normalize_data(self, data):
        self.log.debug(inspect.currentframe().f_code.co_name)
        if isinstance(data, str):
            return {"value": data}
        return data

    def _compute_md5(self, data):
        self.log.debug(inspect.currentframe().f_code.co_name)
        if isinstance(data, str):
            # If it's a string, encode it to first
            return md5(data.encode("raw_unicode_escape")).hexdigest()
        elif not isinstance(data, bytes):
            # If it's neither string nor bytes, convert it to string and then to bytes
            return md5(str(data).encode("raw_unicode_escape")).hexdigest()
        else:
            return md5(data).hexdigest()

    def tag(self):
        return Tag.PE_DOTNET.value

    def extract(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        metadata = {}

        if self.error:
            metadata["Corrupted"] = self.error.args[0]
            dotnet = PEDotNet(metadata)
            self.dotnet = dotnet  # Store for later use in prepare_export_data
            return dotnet  # Return the extracted data instead of exporting directly

        metadata["info"] = {}
        try:
            available_tables = self.dotnet.existent_metadata_tables()
        except Exception as e:
            self.log.error(f"Error getting metadata tables for {self.hash.sha256}: {e}")
            available_tables = []
            metadata["info"]["PotentiallyCorrupted"] = True

        # GUID extraction
        try:
            input_string = self.dotnet.guid_stream_guids[0].string_representation
            
            formatted_uuid = (
                f"{input_string[6:8]}{input_string[4:6]}{input_string[2:4]}{input_string[0:2]}"
                f"-{input_string[10:12]}{input_string[8:10]}"
                f"-{input_string[14:16]}{input_string[12:14]}"
                f"-{input_string[16:20]}"
                f"-{input_string[20:]}"
            )
            metadata["info"]["ModuleVersionID"] = formatted_uuid
        except Exception as e:
            self.log.error(f"Error extracting GUID for {self.hash.sha256}: {e}")

        # CLR Version
        try:
            metadata["info"]["CLRversion"] = self.dotnet.get_runtime_target_version()
        except Exception as e:
            self.log.error(f"Error getting CLR version for {self.hash.sha256}: {e}")

        # Module information
        try:
            if self.dotnet.metadata_table_exists("Module"):
                metadata["info"]["AssemblyModuleName"] = self.dotnet.Module.get_module_name()
        except Exception as e:
            self.log.error(f"Error getting module info for {self.hash.sha256}: {e}")

        # Basic properties
        try:
            metadata["info"].update({
                "IsNativeNgenImage": self.dotnet.is_native_image(),
                "IsMixedAssembly": self.dotnet.is_mixed_assembly(),
                "IsWindowsFormsApp": self.dotnet.is_windows_forms_app(),
                "EntryPointToken": self.dotnet.clr_header.EntryPointToken.value,
                "HasNativeEntryPoint": self.dotnet.has_native_entry_point(),
            })
        except Exception as e:
            self.log.error(f"Error getting basic properties for {self.hash.sha256}: {e}")

        # Assembly flags
        try:
            metadata["info"]["AssemblyFlags"] = self._decode_assembly_flags(
                self.dotnet.clr_header.Flags.value
            )
        except Exception as e:
            self.log.error(f"Error getting assembly flags for {self.hash.sha256}: {e}")

        # More Metadata/Info CLR Header
        try:
            metadata["info"]["NumOfStreams"] = self.dotnet.get_number_of_streams()
            # [TODO] The following two on VT are "RVA entry point"
            #  and "Resources va" respectively. To verify.
            metadata["info"][
                "ResourcesDirectoryAddress"
            ] = self.dotnet.clr_header.ResourcesDirectoryAddress.value
            metadata["info"][
                "ResourcesDirectorySize"
            ] = self.dotnet.clr_header.ResourcesDirectorySize.value
            metadata["info"][
                "StrongNameSignatureAddress"
            ] = self.dotnet.clr_header.StrongNameSignatureAddress.value
            metadata["info"][
                "StrongNameSignatureSize"
            ] = self.dotnet.clr_header.StrongNameSignatureSize.value
            metadata["info"][
                "CodeManagerTableAddress"
            ] = self.dotnet.clr_header.CodeManagerTableAddress.value
            metadata["info"][
                "CodeManagerTableSize"
            ] = self.dotnet.clr_header.CodeManagerTableSize.value
            metadata["info"][
                "VTableFixupsAddress"
            ] = self.dotnet.clr_header.VTableFixupsAddress.value
            metadata["info"][
                "VTableFixupsSize"
            ] = self.dotnet.clr_header.VTableFixupsSize.value
            metadata["info"][
                "ExportAddressTableJumpsAddress"
            ] = self.dotnet.clr_header.ExportAddressTableJumpsAddress.value
            metadata["info"][
                "ExportAddressTableJumpsSize"
            ] = self.dotnet.clr_header.ExportAddressTableJumpsSize.value
            metadata["info"][
                "ManagedNativeHeaderAddress"
            ] = self.dotnet.clr_header.ManagedNativeHeaderAddress.value
            metadata["info"][
                "ManagedNativeHeaderSize"
            ] = self.dotnet.clr_header.ManagedNativeHeaderSize.value
        except Exception as e:
            self.log.error(f"Error getting more metadata/info clr header for {self.hash.sha256}: {e}")

        # Streams section
        try:
            metadata["Streams"] = {}
            stream_names = self.dotnet.get_stream_names()
            for name in stream_names:
                indx = stream_names.index(name)
                stream_header = self.dotnet.dotnet_stream_headers[indx]
                stream_address = self.dotnet.dotnet_streams[indx].address
                metadata["Streams"][name] = {}
                metadata["Streams"][name]["raw_name"] = base64.b64encode(
                    stream_header.Name.value
                ).decode()
                # metadata["Streams"][name]["raw_name"] = name
                metadata["Streams"][name]["size"] = stream_header.Size.value
                # Retrieve the stream data directly using the given address and size
                stream_data = self.pe.get_data(stream_address, stream_header.Size.value)
                metadata["Streams"][name]["entropy"] = (
                    "%.2f" % pefile.SectionStructure.entropy_H(self.pe, stream_data)
                )
                metadata["Streams"][name]["md5"] = md5(stream_data).hexdigest()
        except Exception as e:
            self.log.error(f"Error getting streams for {self.hash.sha256}: {e}")

        # ManifestResource
        try:
            metadata["ManifestResource"] = ()
            if "ManifestResource" in available_tables:
                metadata["info"]["HasManifestResource"] = True
                metadata["ManifestResource"] = (
                    self.dotnet.ManifestResource.get_resource_names()
                )
        except Exception as e:
            self.log.error(f"Error getting manifest resource for {self.hash.sha256}: {e}")

        # ExternalAssemblyRef
        try:
            metadata["ExternalAssemblyRef"] = {}
            if "AssemblyRef" in available_tables:
                metadata["ExternalAssemblyRef"][
                    "names"
                ] = self.dotnet.AssemblyRef.get_assemblyref_names()
                metadata["ExternalAssemblyRef"][
                    "cultures"
                ] = self.dotnet.AssemblyRef.get_assemblyref_cultures()
        except Exception as e:
            self.log.error(f"Error getting external assembly ref for {self.hash.sha256}: {e}")

        # AssemblyData
        try:
            metadata["AssemblyData"] = {}
            if "Assembly" in available_tables:
                metadata["AssemblyData"][
                    "name"
                ] = self.dotnet.Assembly.get_assembly_name()
                # It's officially a one-row table, but there are ITW files with more than one row.
                # It stores information about the current assembly. It is documented in ECMA-335.
                assembly_table = self.dotnet.metadata_tables_lookup[
                    "Assembly"
                ].table_rows[0]
                metadata["AssemblyData"][
                    "MajorVersion"
                ] = assembly_table.MajorVersion.value
                metadata["AssemblyData"][
                    "MinorVersion"
                ] = assembly_table.MinorVersion.value
                metadata["AssemblyData"]["hashalgid"] = assembly_table.HashAlgId.value
                metadata["AssemblyData"][
                    "BuildNumber"
                ] = assembly_table.BuildNumber.value
                metadata["AssemblyData"][
                    "RevisionNumber"
                ] = assembly_table.RevisionNumber.value
                metadata["AssemblyData"][
                    "culture"
                ] = self.dotnet.Assembly.get_assembly_culture()
        except Exception as e:
            self.log.error(f"Error getting assembly data for {self.hash.sha256}: {e}")

        # TypeDef handling
        try:
            metadata["TypeDef"] = {}
            if "TypeDef" in available_tables:
                metadata["info"]["HasTypeDef"] = True
                # Get basic type definitions
                try:
                    # Get all types (ANY visibility)
                    type_defs = self.dotnet.TypeDef.get_type_names()
                    metadata["TypeDef"]["names"] = type_defs if type_defs else []
                    
                    # Get detailed type information with methods
                    types_with_methods = self.dotnet.TypeDef.get_type_names_with_methods()
                    if types_with_methods:
                        metadata["TypeDef"]["detailed"] = []
                        for type_info in types_with_methods:
                            type_data = {
                                "type": type_info.Type,
                                "namespace": type_info.Namespace,
                                "flags": type_info.Flags,
                                "methods": []
                            }
                            for method in type_info.Methods:
                                method_data = {
                                    "name": method.Name,
                                    "flags": method.Flags
                                }
                                if method.Signature:
                                    method_data["signature"] = {
                                        "parameters": method.Signature.get("parameter", []),
                                        "return_type": method.Signature.get("return", ""),
                                        "has_this": method.Signature.get("hasthis", False)
                                    }
                                type_data["methods"].append(method_data)
                            metadata["TypeDef"]["detailed"].append(type_data)
                except AttributeError as e:
                    self.log.warning(f"TypeDef table exists but attributes missing for {self.hash.sha256}: {e}")
                    # metadata["info"]["TypeDefParsingError"] = f"Missing attributes: {str(e)}"
                except Exception as e:
                    self.log.error(f"Error parsing TypeDef table for {self.hash.sha256}: {e}")
                    # metadata["info"]["TypeDefParsingError"] = str(e)
        except Exception as e:
            self.log.error(f"Error handling TypeDef section for {self.hash.sha256}: {e}")
            metadata["TypeDef"] = {"names": [], "detailed": []}
            # metadata["info"]["TypeDefParsingError"] = str(e)

        # ExternalUnmanagedModules
        try:
            metadata["ExternalUnmanagedModules"] = ()
            if "ModuleRef" in available_tables:
                metadata["info"]["HasModuleRef"] = True
                metadata["ExternalUnmanagedModules"] = (
                    self.dotnet.ModuleRef.get_unmanaged_module_names(
                        self.dotnet.Type.UnmanagedModules.RAW
                    )
                )
        except Exception as e:
            self.log.error(f"Error getting external unmanaged modules for {self.hash.sha256}: {e}")

        # ExternalUnmanagedMethods
        try:
            metadata["ExternalUnmanagedMethods"] = ()
            if "ImplMap" in available_tables:
                metadata["info"]["HasImplMap"] = True
                metadata["ExternalUnmanagedMethods"] = (
                    self.dotnet.ImplMap.get_unmanaged_functions()
                )
        except Exception as e:
            self.log.error(f"Error getting external unmanaged methods for {self.hash.sha256}: {e}")

        # Event
        try:
            metadata["Event"] = ()
            if "Event" in available_tables:
                metadata["info"]["HasEvent"] = True
                metadata["Event"] = self.dotnet.Event.get_event_names()
        except Exception as e:
            self.log.error(f"Error getting event for {self.hash.sha256}: {e}")

        # Resources
        try:
            metadata["Resources"] = []
            if self.dotnet.has_resources():
                tmp_resources_list = []
                resource_data = self.dotnet.get_resources()
                for data in resource_data:
                    tmp_dict = {}
                    for resource_item in data.items():
                        if resource_item[0] == "SubResources":
                            if resource_item[1]:
                                tmp_dict["SubResources"] = {}
                                for sub_resource in resource_item[1]:
                                    for sub_resource_item in sub_resource.items():
                                        if sub_resource_item[0] == "Data":
                                            # Check if data is a sequence type that supports len()
                                            if hasattr(sub_resource_item[1], '__len__') and len(sub_resource_item[1]) > 100:
                                                tmp_dict["SubResources"]["Data"] = {}
                                                try:
                                                    # tmp_dict["SubResources"]["Data"][
                                                    #     "md5"
                                                    # ] = md5(
                                                    #     sub_resource_item[1].encode()
                                                    # ).hexdigest()
                                                    tmp_dict["SubResources"]["Data"][
                                                        "md5"
                                                    ] = self._compute_md5(
                                                        sub_resource_item[1]
                                                    )
                                                except Exception as e:
                                                    self.log.error(
                                                        f"Error in dotnet resources"
                                                        f" extraction {self.hash.sha256}: {e}"
                                                    )
                                                guess = magic.from_buffer(
                                                    sub_resource_item[1], mime=True
                                                )
                                                tmp_dict["SubResources"]["Data"][
                                                    "MimeType"
                                                ] = (guess if guess else None)
                                            else:
                                                normalized_data = self._normalize_data(
                                                    sub_resource_item[1].decode()
                                                    if isinstance(
                                                        sub_resource_item[1], bytes
                                                    )
                                                    else sub_resource_item[1]
                                                )
                                                tmp_dict["SubResources"][
                                                    sub_resource_item[0]
                                                ] = normalized_data
                                        else:
                                            tmp_dict["SubResources"][
                                                sub_resource_item[0]
                                            ] = (
                                                sub_resource_item[1].decode()
                                                if isinstance(
                                                    sub_resource_item[1], bytes
                                                )
                                                else sub_resource_item[1]
                                            )
                        elif resource_item[0] == "Data":
                            # Check if data is a sequence type that supports len()
                            if hasattr(resource_item[1], '__len__') and len(resource_item[1]) > 100:
                                tmp_dict["Data"] = {}
                                tmp_dict["Data"]["md5"] = self._compute_md5(
                                    resource_item[1]
                                )
                                guess = magic.from_buffer(resource_item[1], mime=True)
                                tmp_dict["Data"]["MimeType"] = guess if guess else None
                            else:
                                normalized_data = self._normalize_data(
                                    resource_item[1].decode()
                                    if isinstance(resource_item[1], bytes)
                                    else resource_item[1]
                                )
                                tmp_dict["Data"] = normalized_data
                        else:
                            tmp_dict[resource_item[0]] = (
                                resource_item[1].decode()
                                if isinstance(resource_item[1], bytes)
                                else resource_item[1]
                            )
                    tmp_resources_list.append(tmp_dict)
                metadata["Resources"] = tmp_resources_list
        except Exception as e:
            self.log.error(f"Error getting resources for {self.hash.sha256}: {e}")
            metadata["Resources"] = []  # Ensure we always have a valid list even on error

        dotnet = PEDotNet(metadata)
        self.dotnet = dotnet  # Store for later use in prepare_export_data
        return dotnet  # Return the extracted data instead of exporting directly


    def prepare_export_data(self, exporter_type: str) -> Any:
        if exporter_type == "ElasticsearchExporter":
            return self.dotnet
        elif exporter_type == "ClickHouseExporter":
            # Convert metadata to JSON string
            metadata_json = json.dumps(self.dotnet.dotnet)
            
            data = [[
                self.sha256,
                self.md5,
                self.sha1,
                metadata_json,
                datetime.now(timezone.utc)
            ]]
            
            column_names = [
                'sha256', 'md5', 'sha1', 'dotnet', 'analysis_date'
            ]
            
            if not data:
                return None

            column_type_names = [
                'String', 'String', 'String', 'JSON', 'DateTime64(3, \'UTC\')'
            ]

            return (data, column_names, column_type_names)

    def get_clickhouse_table(self) -> str:
        return "redb_pe_dotnet"